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Article ; Online: PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations.

Ahad, S / Lin, C / Reppert, M

2024 Volume 160, Issue 15

Abstract: Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. ... ...

Abstract	Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.
MeSH term(s)	Chlorophyll ; Light-Harvesting Protein Complexes/chemistry ; Circular Dichroism ; Photosynthesis ; Molecular Dynamics Simulation
Chemical Substances	Chlorophyll (1406-65-1) ; Light-Harvesting Protein Complexes
Language	English
Publishing date	2024-04-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0198443
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cu Current Collector with Binder-Free Lithiophilic Nanowire Coating for High Energy Density Lithium Metal Batteries.

Abdul Ahad, Syed / Adegoke, Temilade Esther / Ryan, Kevin M / Geaney, Hugh

Small (Weinheim an der Bergstrasse, Germany)

2023 Volume 19, Issue 20, Page(s) e2207902

Abstract: Despite significant efforts to fabricate high energy density (ED) lithium (Li) metal anodes, problems such as dendrite formation and the need for excess Li (leading to low N/P ratios) have hampered Li metal battery (LMB) development. Here, the use of ... ...

Abstract	Despite significant efforts to fabricate high energy density (ED) lithium (Li) metal anodes, problems such as dendrite formation and the need for excess Li (leading to low N/P ratios) have hampered Li metal battery (LMB) development. Here, the use of germanium (Ge) nanowires (NWs) directly grown on copper (Cu) substrates (Cu-Ge) to induce lithiophilicity and subsequently guide Li ions for uniform Li metal deposition/stripping during electrochemical cycling is reported. The NW morphology along with the formation of the Li
Language	English
Publishing date	2023-02-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2168935-0
ISSN	1613-6829 ; 1613-6810
ISSN (online)	1613-6829
ISSN	1613-6810
DOI	10.1002/smll.202207902
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Description of a new species of the genus Caveonchus Siddiqi, 1982 (Nematoda: Dorylaimida) with diagnostic compendium and key to its species

Ahad, S / W. Ahmad

Helminthologia. 2017 June 27, v. 54, no. 2

2017

Abstract: Caveonchus siddiqii n. sp. is described and illustrated based on specimens collected from both India and Japan. It is characterized by having a medium sized body (L= 0.86 - 1.12 mm); labial disc present; amphideal fovea flask-shaped; lip region cap-like, ...

Abstract	Caveonchus siddiqii n. sp. is described and illustrated based on specimens collected from both India and Japan. It is characterized by having a medium sized body (L= 0.86 - 1.12 mm); labial disc present; amphideal fovea flask-shaped; lip region cap-like, offset by slight constriction; odontostyle 8 - 9 μm, odontophore 10 - 12 μm; pharynx with slender anterior part which expands abruptly into the saccate basal bulb, occupying about 16 - 21 % of total neck length; female genital system mono-opisthodelphic; anterior genital branch 70 - 100 μm or 1.9 - 2.8 times the midbody diameter long; tail short, rounded, hemispheroid, 0.5 - 0.7 anal body diameter long; spicules 30 - 38 μm long; and three spaced ventromedian supplements. Its relationship with all the known species of the genus is discussed. A diagnostic compendium and a key to identification of the species is also provided.
Keywords	Dorylaimida ; female genitalia ; neck ; new species ; pharynx ; scientific illustration ; tail ; taxon descriptions ; India ; Japan
Language	English
Dates of publication	2017-0627
Size	p. 145-151.
Publishing place	De Gruyter Open
Document type	Article
ISSN	1336-9083
DOI	10.1515/helm-2017-0018
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Artificial Intelligence and Machine Learning in Optical Information Processing: introduction to the feature issue.

Iftekharuddin, Khan / Preza, Chrysanthe / Awwal, Abdul Ahad S / Zelinski, Michael E

Applied optics

2022 Volume 61, Issue 7, Page(s) AIML1

Abstract: This special feature issue covers the intersection of topical areas in artificial intelligence (AI)/machine learning (ML) and optics. The papers broadly span the current state-of-the-art advances in areas including image recognition, signal and image ... ...

Abstract	This special feature issue covers the intersection of topical areas in artificial intelligence (AI)/machine learning (ML) and optics. The papers broadly span the current state-of-the-art advances in areas including image recognition, signal and image processing, machine inspection/vision and automotive as well as areas of traditional optical sensing, interferometry and imaging.
Language	English
Publishing date	2022-03-14
Publishing country	United States
Document type	Journal Article
ISSN	1539-4522
ISSN (online)	1539-4522
DOI	10.1364/AO.456405
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Binder-free germanium nanoparticle decorated multi-wall carbon nanotube anodes prepared

Pham, Xuan-Manh / Abdul Ahad, Syed / Patil, Niraj Nitish / Geaney, Hugh / Singh, Shalini / Ryan, Kevin M

Nanoscale horizons

2024 Volume 9, Issue 4, Page(s) 637–645

Abstract: Germanium (Ge) has a high theoretical specific capacity (1384 mA h ... ...

Abstract	Germanium (Ge) has a high theoretical specific capacity (1384 mA h g
Language	English
Publishing date	2024-03-25
Publishing country	England
Document type	Journal Article
ISSN	2055-6764
ISSN (online)	2055-6764
DOI	10.1039/d3nh00501a
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Solution processable Si/Ge heterostructure NWs enabling anode mass reduction for practical full-cell Li-ion batteries.

Adegoke, Temilade Esther / Abdul Ahad, Syed / Bangert, Ursel / Geaney, Hugh / Ryan, Kevin M

Nanoscale advances

2023 Volume 5, Issue 23, Page(s) 6514–6523

Abstract: Here, we report the solution phase synthesis of axial heterostructure Si and Ge (hSG) nanowires (NWs). The NWs were grown in a high boiling point solvent from a low-cost Sn powder to achieve a powder form product which represents an attractive route from ...

Abstract	Here, we report the solution phase synthesis of axial heterostructure Si and Ge (hSG) nanowires (NWs). The NWs were grown in a high boiling point solvent from a low-cost Sn powder to achieve a powder form product which represents an attractive route from lab-scale to commercial application. Slurry processed anodes of the NWs were investigated in half-cell (
Language	English
Publishing date	2023-09-01
Publishing country	England
Document type	Journal Article
ISSN	2516-0230
ISSN (online)	2516-0230
DOI	10.1039/d3na00648d
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A propensity matched comparison of robotic

Rufa, Magdalena / Nagib, Ragi / Aktuerk, Dincer / Ahad, Samir / Ghinescu, Mihnea / Franke, Ulrich

Journal of thoracic disease

2023 Volume 15, Issue 12, Page(s) 6459–6474

Abstract: Background: Atrial fibrillation (AF) occurs frequently in patients with mitral valve disease. Results of cryoablation concomitant with either minimally invasive video-assisted [minimally invasive mitral valve surgery (MIMVS)] or with robotic-assisted ( ... ...

Abstract	Background: Atrial fibrillation (AF) occurs frequently in patients with mitral valve disease. Results of cryoablation concomitant with either minimally invasive video-assisted [minimally invasive mitral valve surgery (MIMVS)] or with robotic-assisted (RMV) mitral valve surgery have previously been separately reported. However, there are up-to-date no studies comparing the two procedures in terms of safety, efficacy, and mid-term follow-up. Methods: Between January 2017 and March 2022, 294 patients underwent MIMVS, and 187 patients underwent RMV at our institution. After 1:1 propensity score matching using 22 preoperative variables, the study included 104 patients. Group 1 (MIMVS) included 52 patients operated on between 2017-2022 using a minimally invasive video-assisted right-sided mini-thoracotomy. Group 2 (RMV) included 52 patients operated on between 2019-2021 using a robotic-assisted approach. Early and mid-term outcomes were assessed, including maintenance of sinus rhythm. Follow-up was 100% complete at a median follow-up of 2 years. Results: For the entire propensity matched cohort, the median EuroSCORE II was 3.14 [interquartile range (IQR), 1.93-4.99], the median age was 68 (IQR, 61-74) years, and two thirds of the patients were male. Most (72.1%) underwent mitral valve surgery, and 26.9% had an additional tricuspid procedure. Only four patients underwent mitral valve replacement (3.8%). The majority (87.5%) received a left-sided atrial Maze and 12.5% a bi-atrial Maze. The left atrial appendage was occluded in 72.1% cases. Overall, there were no significant differences between the two propensity matched groups in baseline demographics or intra-operative characteristics. Similarly, there were no significant differences in the post-operative short and mid-term outcomes between the two groups. There were no in-hospital or 30-day deaths. At the mid-term survival was similar between groups, log-rank test P=0.056. Maintenance of sinus rhythm at follow-up was 76%. Conclusions: Mitral or double valve repair with concomitant cryoablation can be safely performed with either a MIMVS or RMV approach. Both methods demonstrated outstanding early and mid-term outcomes.
Language	English
Publishing date	2023-12-05
Publishing country	China
Document type	Journal Article
ZDB-ID	2573571-8
ISSN	2077-6624 ; 2072-1439
ISSN (online)	2077-6624
ISSN	2072-1439
DOI	10.21037/jtd-23-1306
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Caffeine Consumption and Depression, Anxiety, and Stress Levels Among University Students in Medina: A Cross-Sectional Study.

Makki, Nadir M / Alharbi, Shouq T / Alharbi, Abdulrahman M / Alsharif, Ahad S / Aljabri, Ahmed M

Cureus

2023 Volume 15, Issue 10, Page(s) e48018

Abstract: Introduction Caffeine is a psychoactive stimulant frequently found in coffee, tea, energy drinks, and some medications. Various mental health challenges, including stress, anxiety, and depression, commonly affect college students. Moreover, an individual' ...

Abstract	Introduction Caffeine is a psychoactive stimulant frequently found in coffee, tea, energy drinks, and some medications. Various mental health challenges, including stress, anxiety, and depression, commonly affect college students. Moreover, an individual's mental and physical health can be significantly impacted by stress, anxiety, and depression. However, the impact of caffeine on mental health, particularly its association with depressive and anxiety symptoms, remains inconclusive. Thus, this study aimed to evaluate the amount of caffeine consumed by university students and its association with depression, anxiety, and stress levels. Material and method This cross-sectional study was performed on Taibah University students in Medina from both health-related and non-health-related colleges. We used a self-administrated questionnaire composed of four sections: the informed consent section; sociodemographic information; the Depression, Anxiety, and Stress Scale (DASS-21), which assessed the depression, anxiety, and stress levels; and a caffeine-measuring questionnaire, which reported daily caffeine intake in milligrams per day. Result This cross-sectional study examined a 520 convenience sample of Taibah University students with an age range from 17 to 29 years. The majority of the participants were single (95.2%), most of them were female (73.8%), and slightly more than half (51.5%) were recruited from health-related colleges. According to the study's DASS-21 score results, 45.8% of the students had extremely severe stress, 61% had extremely severe anxiety, and 51% had extremely severe depression. The most frequently reported sources of daily caffeine among the participants were Arabic coffee (69.6%), specialty coffee (57.5%), black tea (56.3%), cola (48.7%), and regular coffee (48.5%). The overall daily amount of consumed caffeine ranged from zero to 4276.7 mg/oz. However, no significant association was found between the severity of the DASS-21 score and the daily consumption of caffeine among Taibah University students. Conclusion Our study shows no significant association between the severity of depression, anxiety, and stress and daily caffeine consumption among university students. This proves the opposite of the theory that high levels of caffeine consumption can be correlated to high levels of depression, stress, and anxiety.
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.48018
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Description of a new species of the genus Caveonchus Siddiqi, 1982 (Nematoda

Ahad S. / Ahmad W.

Helminthologia, Vol 54, Iss 2, Pp 145-

Dorylaimida) with diagnostic compendium and key to its species

2017 Volume 151

Abstract	Caveonchus siddiqii n. sp. is described and illustrated based on specimens collected from both India and Japan. It is characterized by having a medium sized body (L= 0.86 - 1.12 mm); labial disc present; amphideal fovea flask-shaped; lip region cap-like, offset by slight constriction; odontostyle 8 - 9 μm, odontophore 10 - 12 μm; pharynx with slender anterior part which expands abruptly into the saccate basal bulb, occupying about 16 - 21 % of total neck length; female genital system mono-opisthodelphic; anterior genital branch 70 - 100 μm or 1.9 - 2.8 times the midbody diameter long; tail short, rounded, hemispheroid, 0.5 - 0.7 anal body diameter long; spicules 30 - 38 μm long; and three spaced ventromedian supplements. Its relationship with all the known species of the genus is discussed. A diagnostic compendium and a key to identification of the species is also provided.
Keywords	caveonchus siddiqii n. sp ; compendium ; description ; india ; japan ; Agriculture (General) ; S1-972 ; Medicine (General) ; R5-920
Subject code	590
Language	English
Publishing date	2017-06-01T00:00:00Z
Publisher	Sciendo
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Description of two new and two known species of the Genus Tylencholaimellus Cobb in M. V. Cobb, 1915 (Nematoda: Dorylaimida: Tylencholaimoidea).

Ahmad, Wasim / Ahad, Sumaya

Zootaxa

2018 Volume 4375, Issue 3, Page(s) 301–324

Abstract: Two new and two known species of the dorylaimid nematode genus Tylencholaimellus Cobb in M.V. Cobb, 1915 are described and illustrated. Tylencholaimellus arabicus sp. n. collected from Saudi Arabia is characterized by having small sized body (L= 0.66-0 ... ...

Abstract	Two new and two known species of the dorylaimid nematode genus Tylencholaimellus Cobb in M.V. Cobb, 1915 are described and illustrated. Tylencholaimellus arabicus sp. n. collected from Saudi Arabia is characterized by having small sized body (L= 0.66-0.83 mm); outer cuticle with distinct transverse striations; inner layer thick with fine transverse striations; lip region offset by a deep constriction, inner liplets slightly raised; odontostyle 15-17 µm, odontophore 8-10 µm, combined length 25-26 μm; female genital system mono-opisthodelphic; anterior uterine sac 0.5-1.3 times midbody diameter in length; transverse vulva and short conoid tail Tylencholaimellus masakii sp. n. collected from Japan is characterized by having small sized body (L= 0.77-0.81 mm); lip region offset by a slight constriction; labial disc present; odontostyle 11-12 µm, odontophore 6-7 µm, combined length 18-18.5 μm; female genital system mono-opisthodelphic; anterior uterine sac 1.1-1.8 midbody diameter long; transverse vulva and rounded-conoid tail. Tylencholaimellus striatus Thorne, 1939 and T. projectus Siddiqi, 1964 are redescribed based on material collected from India. A diagnostic compendium of the genus Tylencholaimellus is also provided.
MeSH term(s)	Animals ; Female ; India ; Japan ; Nematoda ; Saudi Arabia ; Uterus
Language	English
Publishing date	2018-01-25
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.4375.3.1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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