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Book ; Online: Energy Patterns for Web

Rani, Pooja / Zellweger, Jonas / Kousadianos, Veronika / Cruz, Luis / Kehrer, Timo / Bacchelli, Alberto

An Exploratory Study

2024

Abstract: As the energy footprint generated by software is increasing at an alarming rate, understanding how to develop energy-efficient applications has become a necessity. Previous work has introduced catalogs of coding practices, also known as energy patterns. ... ...

Abstract	As the energy footprint generated by software is increasing at an alarming rate, understanding how to develop energy-efficient applications has become a necessity. Previous work has introduced catalogs of coding practices, also known as energy patterns. These patterns are yet limited to Mobile or third-party libraries. In this study, we focus on the Web domain--a main source of energy consumption. First, we investigated whether and how Mobile energy patterns could be ported to this domain and found that 20 patterns could be ported. Then, we interviewed six expert web developers from different companies to challenge the ported patterns. Most developers expressed concerns for antipatterns, specifically with functional antipatterns, and were able to formulate guidelines to locate these patterns in the source code. Finally, to quantify the effect of Web energy patterns on energy consumption, we set up an automated pipeline to evaluate two ported patterns: 'Dynamic Retry Delay' (DRD) and 'Open Only When Necessary' (OOWN). With this, we found no evidence that the DRD pattern consumes less energy than its antipattern, while the opposite is true for OOWN. Data and Material: https://doi.org/10.5281/zenodo.8404487
Keywords	Computer Science - Software Engineering ; Computer Science - Performance
Subject code	690
Publishing date	2024-01-12
Publishing country	us
Document type	Book ; Online
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Article ; Online: The Association between Postural Sway and Preclinical Alzheimer Disease among Community-Dwelling Older Adults.

Bollinger, Rebecca M / Chen, Szu-Wei / Krauss, Melissa J / Keleman, Audrey A / Kehrer-Dunlap, Abigail / Kaesler, Megan / Ances, Beau M / Stark, Susan L

The journals of gerontology. Series A, Biological sciences and medical sciences

2024

Abstract: ... with preclinical AD (DTC path length mean difference 19.8, 95% CI 2.6 to 37.0, t(201)=2.29, p=0.024). Greater DTC ...

Abstract	Background: It is unknown whether older adults with preclinical Alzheimer disease (AD) experience changes in postural sway compared to those without preclinical AD. The purpose of this study was to understand the effect of dual tasking on standing balance, or postural sway, for people with and without preclinical AD. Methods: A cross-sectional analysis of baseline data from a longitudinal cohort study. Participants were cognitively normal older adults with and without preclinical AD. Postural sway (path length) was tested using a force plate under standard and dual task balance conditions. Dual task cost (DTC) was calculated to examine performance change in balance conditions. Logistic regression models were used to predict preclinical AD status as a function of DTC. Results: 203 participants (65 preclinical AD+) were included. DTC for path length was significantly greater for participants with preclinical AD (DTC path length mean difference 19.8, 95% CI 2.6 to 37.0, t(201)=2.29, p=0.024). Greater DTC was significantly associated with increased odds of having preclinical AD (adjusted odds ratio for a 20-unit increase in DTC 1.16, 95% CI 1.02 to 1.32). Conclusions: Older adults with preclinical AD are more likely to demonstrate significantly greater DTC in postural sway than those without preclinical AD. Dual tasking should be integrated into balance and fall risk assessments and may inform early detection of preclinical AD.
Language	English
Publishing date	2024-03-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1223643-3
ISSN	1758-535X ; 1079-5006
ISSN (online)	1758-535X
ISSN	1079-5006
DOI	10.1093/gerona/glae091
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Article ; Online: Physiological jump in erythrocyte redox potential during Plasmodium falciparum development occurs independent of the sickle cell trait.

Haag, Marvin / Kehrer, Jessica / Sanchez, Cecilia P / Deponte, Marcel / Lanzer, Michael

Redox biology

2022 Volume 58, Page(s) 102536

Abstract: ... for the export of disulfide-containing proteins. In summary, P. falciparum blood stage development from the late ...

Abstract	The redox state of the host-parasite unit has been hypothesized to play a central role for the fitness of the intraerythrocytic blood stages of the human malaria parasite Plasmodium falciparum. In particular, hemoglobinopathies have been suggested to cause a more oxidizing environment, thereby protecting from severe malaria. Here we determined the redox potential of infected wild-type (hemoglobin AA) or sickle trait (hemoglobin AS) erythrocytes using parasite-encoded variants of the redox-sensitive green-fluorescent protein 2 (roGFP2). Our non-invasive roGFP2 single-cell measurements revealed a reducing steady-state redox potential of -304 ± 11 mV for the erythrocyte cytosol during ring-stage development and a rather sudden oxidation to -278 ± 12 mV during trophozoite-stage development around 28 h post invasion. There was no significant difference between wild-type or sickle trait erythrocytes regarding the stage dependence and the detected increase of the redox potential during the intraerythrocytic life cycle. The steady-state redox potential of the parasite cytosol, between -304 and -313 mV, was highly reducing throughout the life cycle. The redox potential in the parasitophorous vacuole at the interface between the secretory pathway and the erythrocyte was -284 ± 10 mV and remained stable during trophozoite-stage development with implications for the export of disulfide-containing proteins. In summary, P. falciparum blood stage development from the late ring to the early trophozoite stage causes a physiological jump in erythrocyte redox potential irrespective of the presence or absence of hemoglobin S.
Language	English
Publishing date	2022-11-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2701011-9
ISSN	2213-2317 ; 2213-2317
ISSN (online)	2213-2317
ISSN	2213-2317
DOI	10.1016/j.redox.2022.102536
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Article ; Online: Identification of an

Büki, Gergely / Bekő, Anna / Bödör, Csaba / Urbán, Péter / Németh, Krisztina / Hadzsiev, Kinga / Fekete, György / Kehrer-Sawatzki, Hildegard / Bene, Judit

International journal of molecular sciences

2023 Volume 24, Issue 17

Abstract: Neurofibromatosis type 1 (NF1) is a clinically heterogeneous neurocutaneous disorder inherited in autosomal dominant manner. Approximately 5-10% of the cases are caused ... ...

Abstract	Neurofibromatosis type 1 (NF1) is a clinically heterogeneous neurocutaneous disorder inherited in autosomal dominant manner. Approximately 5-10% of the cases are caused by
MeSH term(s)	Humans ; Neurofibromatosis 1/genetics ; DNA Copy Number Variations ; Genes, Neurofibromatosis 1 ; Megalencephaly ; Chromosome Mapping
Language	English
Publishing date	2023-09-01
Publishing country	Switzerland
Document type	Case Reports ; Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241713580
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Article ; Online: Revealing the dynamics of ultrarelativistic non-equilibrium many-electron systems with phase space tomography.

Funkner, Stefan / Niehues, Gudrun / Nasse, Michael J / Bründermann, Erik / Caselle, Michele / Kehrer, Benjamin / Rota, Lorenzo / Schönfeldt, Patrik / Schuh, Marcel / Steffen, Bernd / Steinmann, Johannes L / Weber, Marc / Müller, Anke-Susanne

Scientific reports

2023 Volume 13, Issue 1, Page(s) 4618

Abstract: The description of physical processes with many-particle systems is a key approach to the modeling of numerous physical systems. For example in storage rings, where ultrarelativistic particles are agglomerated in dense bunches, the modeling and ... ...

Abstract	The description of physical processes with many-particle systems is a key approach to the modeling of numerous physical systems. For example in storage rings, where ultrarelativistic particles are agglomerated in dense bunches, the modeling and measurement of their phase-space distribution is of paramount importance: at any time the phase-space distribution not only determines the complete space-time evolution but also provides fundamental performance characteristics for storage ring operation. Here, we demonstrate a non-destructive tomographic imaging technique for the 2D longitudinal phase-space distribution of ultrarelativistic electron bunches. For this purpose, we utilize a unique setup, which streams turn-by-turn near-field measurements of bunch profiles at MHz repetition rates. To demonstrate the feasibility of our method, we induce a non-equilibrium state and show that the phase-space distribution microstructuring as well as the phase-space distribution dynamics can be observed in great detail. Our approach offers a pathway to control ultrashort bunches and supports, as one example, the development of compact accelerators with low energy footprints.
Language	English
Publishing date	2023-03-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-31196-5
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Article: Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing.

Cohen, Phillip / DeGrace, Emma J / Danziger, Oded / Patel, Roosheel S / Barrall, Erika A / Bobrowski, Tesia / Kehrer, Thomas / Cupic, Anastasija / Miorin, Lisa / García-Sastre, Adolfo / Rosenberg, Brad R

bioRxiv : the preprint server for biology

2023

Abstract: ... GEM Single Cell V(D)J (10X 5') sequencing, we find that 10X 5' with an extended read 1 (R1) sequencing ...

Abstract	Single cell RNA sequencing (scRNA-Seq) studies have provided critical insight into the pathogenesis of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), the causative agent of COronaVIrus Disease 2019 (COVID-19). scRNA-Seq workflows are generally designed for the detection and quantification of eukaryotic host mRNAs and not viral RNAs. Here, we compare different scRNA-Seq methods for their ability to quantify and detect SARS-CoV-2 RNAs with a focus on subgenomic mRNAs (sgmRNAs). We present a data processing strategy, single cell CoronaVirus sequencing (scCoVseq), which quantifies reads unambiguously assigned to sgmRNAs or genomic RNA (gRNA). Compared to standard 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') and Chromium Next GEM Single Cell V(D)J (10X 5') sequencing, we find that 10X 5' with an extended read 1 (R1) sequencing strategy maximizes the detection of sgmRNAs by increasing the number of unambiguous reads spanning leader-sgmRNA junction sites. Using this method, we show that viral gene expression is highly correlated across cells suggesting a relatively consistent proportion of viral sgmRNA production throughout infection. Our method allows for quantification of coronavirus sgmRNA expression at single-cell resolution, and thereby supports high resolution studies of the dynamics of coronavirus RNA synthesis.
Language	English
Publishing date	2023-02-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.11.22.469642
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Article ; Online: Artificial intelligence-enabled simulation of gluteal augmentation: A helpful tool in preoperative outcome simulation?

Knoedler, Leonard / Odenthal, Jan / Prantl, Lukas / Oezdemir, Berkin / Kehrer, Andreas / Kauke-Navarro, Martin / Matar, Dany Y / Obed, Doha / Panayi, Adriana C / Broer, P Niclas / Chartier, Christian / Knoedler, Samuel

Journal of plastic, reconstructive & aesthetic surgery : JPRAS

2023 Volume 80, Page(s) 94–101

Abstract: Background: While the buttock region is considered an esthetic hallmark, the Brazilian butt lift (BBL) remains controversially discussed in the plastic surgery community. This is due to its contentious safety profile. Thus, informed consent and patient ... ...

Abstract	Background: While the buttock region is considered an esthetic hallmark, the Brazilian butt lift (BBL) remains controversially discussed in the plastic surgery community. This is due to its contentious safety profile. Thus, informed consent and patient education play a key role in preoperative planning. To this end, we aimed to program an easy-to-use, widely accessible, and low-budget algorithm that produces reliable outcome simulations. Methods: The conditional generative adversarial network (GAN) was trained using pre- and postoperative images from 1628 BBL patients. To validate outcome simulation, 25 GAN-generated images were assessed deploying 67 Amazon Mechanical Turk Workers (Mturks). Results: Mturks could not differentiate between GAN-generated and real patient images in approximately 49.4% of all trials. Conclusion: This study presents a free-to-use, widely accessible, and reliable algorithm to visualize potential surgical outcomes that could potentially be applied in other fields of plastic surgery.
MeSH term(s)	Humans ; Artificial Intelligence ; Plastic Surgery Procedures ; Surgical Flaps/surgery ; Algorithms ; Buttocks/surgery
Language	English
Publishing date	2023-02-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2217750-4
ISSN	1878-0539 ; 1748-6815 ; 0007-1226
ISSN (online)	1878-0539
ISSN	1748-6815 ; 0007-1226
DOI	10.1016/j.bjps.2023.01.039
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Article ; Online: Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing.

Cohen, Phillip / DeGrace, Emma J / Danziger, Oded / Patel, Roosheel S / Barrall, Erika A / Bobrowski, Tesia / Kehrer, Thomas / Cupic, Anastija / Miorin, Lisa / García-Sastre, Adolfo / Rosenberg, Brad R

Microbiology spectrum

2023 , Page(s) e0077623

Abstract: ... Genomics Chromium Next GEM Single Cell V(D)J (10X 5') libraries sequenced with standard read configurations ...

Abstract	Single-cell RNA sequencing (scRNA-Seq) studies have provided critical insight into the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). scRNA-Seq library preparation methods and data processing workflows are generally designed for the detection and quantification of eukaryotic host mRNAs and not viral RNAs. Here, we compare different scRNA-Seq library preparation methods for their ability to quantify and detect SARS-CoV-2 RNAs with a focus on subgenomic mRNAs (sgmRNAs). We show that compared to 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') libraries or 10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5') libraries sequenced with standard read configurations, 10X 5' libraries sequenced with an extended length read 1 (R1) that covers both cell barcode and transcript sequence (termed "10X 5' with extended R1") increase the number of unambiguous reads spanning leader-sgmRNA junction sites. We further present a data processing workflow, single-cell coronavirus sequencing (scCoVseq), which quantifies reads unambiguously assigned to viral sgmRNAs or viral genomic RNA (gRNA). We find that combining 10X 5' with extended R1 library preparation/sequencing and scCoVseq data processing maximizes the number of viral UMIs per cell quantified by scRNA-Seq. Corresponding sgmRNA expression levels are highly correlated with expression in matched bulk RNA-Seq data sets quantified with established tools for SARS-CoV-2 analysis. Using this scRNA-Seq approach, we find that SARS-CoV-2 gene expression is highly correlated across individual infected cells, which suggests that the proportion of viral sgmRNAs remains generally consistent throughout infection. Taken together, these results and corresponding data processing workflow enable robust quantification of coronavirus sgmRNA expression at single-cell resolution, thereby supporting high-resolution studies of viral RNA processes in individual cells. IMPORTANCE Single-cell RNA sequencing (scRNA-Seq) has emerged as a valuable tool to study host-virus interactions, especially for coronavirus disease 2019 (COVID-19). Here we compare the performance of different scRNA-Seq library preparation methods and sequencing strategies to detect SARS-CoV-2 RNAs and develop a data processing workflow to quantify unambiguous sequence reads derived from SARS-CoV-2 genomic RNA and subgenomic mRNAs. After establishing a workflow that maximizes the detection of SARS-CoV-2 subgenomic mRNAs, we explore patterns of SARS-CoV-2 gene expression across cells with variable levels of total viral RNA, assess host gene expression differences between infected and bystander cells, and identify non-canonical and lowly abundant SARS-CoV-2 RNAs. The sequencing and data processing strategies developed here can enhance studies of coronavirus RNA biology at single-cell resolution and thereby contribute to our understanding of viral pathogenesis.
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.00776-23
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Article: Environmental risk assessment of biocidal products: identification of relevant components and reliability of a component-based mixture assessment.

Coors, Anja / Vollmar, Pia / Heim, Jennifer / Sacher, Frank / Kehrer, Anja

Environmental sciences Europe

2018 Volume 30, Issue 1, Page(s) 3

Abstract: Background: Biocidal products are mixtures of one or more active substances (a.s.) and a broad range of formulation additives. There is regulatory guidance currently under development that will specify how the combined effects of the a.s. and any ... ...

Abstract	Background: Biocidal products are mixtures of one or more active substances (a.s.) and a broad range of formulation additives. There is regulatory guidance currently under development that will specify how the combined effects of the a.s. and any relevant formulation additives shall be considered in the environmental risk assessment of biocidal products. The default option is a component-based approach (CBA) by which the toxicity of the product is predicted from the toxicity of 'relevant' components using concentration addition. Hence, unequivocal and practicable criteria are required for identifying the 'relevant' components to ensure protectiveness of the CBA, while avoiding unnecessary workload resulting from including by default components that do not significantly contribute to the product toxicity. The present study evaluated a set of different criteria for identifying 'relevant' components using confidential information on the composition of 21 wood preservative products. Theoretical approaches were complemented by experimentally testing the aquatic toxicity of seven selected products. Results: For three of the seven tested products, the toxicity was underestimated for the most sensitive endpoint (green algae) by more than factor 2 if only the a.s. were considered in the CBA. This illustrated the necessity of including at least some additives along with the a.s. Considering additives that were deemed 'relevant' by the tentatively established criteria reduced the underestimation of toxicity for two of the three products. A lack of data for one specific additive was identified as the most likely reason for the remaining toxicity underestimation of the third product. In three other products, toxicity was overestimated by more than factor 2, while prediction and observation fitted well for the seventh product. Considering all additives in the prediction increased only the degree of overestimation. Conclusions: Supported by theoretical calculations and experimental verifications, the present study developed criteria for the identification of CBA-relevant components in a biocidal product. These criteria are based on existing criteria stated in the regulation for classification, labelling and packaging of substances. The CBA was found sufficiently protective and reliable for the tested products when applying the here recommended criteria. The lack of available aquatic toxicity data for some of the identified relevant components was the main reason for underestimation of product toxicity.
Language	English
Publishing date	2018-01-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2593962-2
ISSN	2190-4715 ; 2190-4707
ISSN (online)	2190-4715
ISSN	2190-4707
DOI	10.1186/s12302-017-0130-0
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Article ; Online: The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection.

Fernández, Jose Javier / Marín, Arturo / Rosales, Romel / Penrice-Randal, Rebekah / Mlcochova, Petra / Alvarez, Yolanda / Villalón-Letelier, Fernando / Yildiz, Soner / Pérez, Enrique / Rathnasinghe, Raveen / Cupic, Anastasija / Kehrer, Thomas / Uccellini, Melissa B / Alonso, Sara / Martínez, Fernando / McGovern, Briana Lynn / Clark, Jordan J / Sharma, Parul / Bayón, Yolanda /

Alonso, Andrés / Albrecht, Randy A / White, Kris M / Schotsaert, Michael / Miorin, Lisa / Stewart, James P / Hiscox, Julian A / Gupta, Ravindra K / Irigoyen, Nerea / García-Sastre, Adolfo / Crespo, Mariano Sánchez / Fernández, Nieves

Biochimica et biophysica acta. Molecular basis of disease

2024 Volume 1870, Issue 5, Page(s) 167193

Abstract: SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state ... ...

Abstract	SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.
Language	English
Publishing date	2024-04-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	60-7
ISSN	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbadis.2024.167193
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