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  1. Article ; Online: A Case Report of Acute Prostatitis Secondary to Use of P-valve Condom Catheter During Cave Diving.

    Barash, Ashley / Stern, Evan / Hoelle, Robyn

    Clinical practice and cases in emergency medicine

    2021  Volume 5, Issue 4, Page(s) 436–439

    Abstract: ... Aeromonas hydrophila/A. caviae. His disease process was later recognized as a complication of the use of a P-valve ... of prostatitis as a result of the use of a P-valve condom catheter while diving. Furthermore, the pathogen ...

    Abstract Introduction: Acute bacterial prostatitis is characterized by acute inflammation of the prostate gland accompanied by the presence of pain and other urinary tract or systemic symptoms. Prostatitis is a relatively common disease of the urinary tract in men, However, this case reports a man diagnosed with acute bacterial prostatitis with an unusual presentation, as well as an unusual pathogen and a unique mechanism of colonization.
    Case report: A 52-year-old male with no past medical history presented to our facility for right-sided buttock pain associated with dysuria, diarrhea, and perianal burning. The patient was diagnosed with sepsis secondary to acute bacterial prostatitis, and the pathogen identified in his urine was Aeromonas hydrophila/A. caviae. His disease process was later recognized as a complication of the use of a P-valve condom catheter while freshwater cave diving.
    Conclusion: This is the first documented case of prostatitis as a result of the use of a P-valve condom catheter while diving. Furthermore, the pathogen identified is of particular interest as there are very few documented cases of urosepsis secondary to Aeromonas hydrophila or A. caviae.
    Language English
    Publishing date 2021-11-23
    Publishing country United States
    Document type Journal Article
    ISSN 2474-252X
    ISSN (online) 2474-252X
    DOI 10.5811/cpcem.2021.7.52639
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  2. Article ; Online: Glycosaminoglycans as Tools to Decipher the Platelet Tumor Cell Interaction: A Focus on P-Selectin.

    Schwarz, Svenja / Gockel, Lukas Maria / Naggi, Annamaria / Barash, Uri / Gobec, Martina / Bendas, Gerd / Schlesinger, Martin

    Molecules (Basel, Switzerland)

    2020  Volume 25, Issue 5

    Abstract: ... confirmed that only those heparin derivatives with P-selectin blocking capacities were able to attenuate ... Furthermore, a role of P-selectin in platelet activation and signaling could be confirmed by proteome profiler ... coagulation. Moreover, we identify platelet P-selectin, which obviously acts as molecular switch and controls ...

    Abstract Tumor cell-platelet interactions are regarded as an initial crucial step in hematogenous metastasis. Platelets protect tumor cells from immune surveillance in the blood, mediate vascular arrest, facilitate tumor extravasation, growth, and finally angiogenesis in the metastatic foci. Tumor cells aggregate platelets in the bloodstream by activation of the plasmatic coagulation cascade and by direct contact formation. Antimetastatic activities of unfractionated or low molecular weight heparin (UFH/LMWH) can undoubtedly be related to attenuated platelet activation, but molecular mechanisms and contribution of contact formation vs. coagulation remain to be elucidated. Using a set of non-anticoagulant heparin derivatives varying in size or degree of sulfation as compared with UFH, we provide insight into the relevance of contact formation for platelet activation. Light transmission aggregometry and ATP release assays confirmed that only those heparin derivatives with P-selectin blocking capacities were able to attenuate breast cancer cell-induced platelet activation, while pentasaccharide fondaparinux was without effects. Furthermore, a role of P-selectin in platelet activation and signaling could be confirmed by proteome profiler arrays detecting platelet kinases. In this study, we demonstrate that heparin blocks tumor cell-induced coagulation. Moreover, we identify platelet P-selectin, which obviously acts as molecular switch and controls aggregation and secretion of procoagulant platelets.
    MeSH term(s) Blood Platelets/drug effects ; Blood Platelets/pathology ; Breast Neoplasms/pathology ; Cell Communication/drug effects ; Cell Line, Tumor ; Cell Shape/drug effects ; Cytoplasmic Granules/drug effects ; Cytoplasmic Granules/metabolism ; Glycosaminoglycans/pharmacology ; Heparin/pharmacology ; Humans ; Neoplasms/pathology ; P-Selectin/metabolism ; Platelet Activation/drug effects ; Platelet Aggregation/drug effects ; Signal Transduction/drug effects
    Chemical Substances Glycosaminoglycans ; P-Selectin ; Heparin (9005-49-6)
    Language English
    Publishing date 2020-02-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules25051039
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  3. Article ; Online: The use of machine learning for the determination of a type/model of firearms by the characteristics on cartridge cases.

    Giverts, Pavel / Sorokina, Ksenia / Barash, Mark / Fedorenko, Vladimir

    Forensic science international

    2024  Volume 358, Page(s) 112021

    Abstract: Cartridge cases are commonly collected at crime scenes involving firearms. One of the stages in forensic examination is the determination of the type and model of firearms based on the class characteristics of these cartridge cases. A firearm examiner ... ...

    Abstract Cartridge cases are commonly collected at crime scenes involving firearms. One of the stages in forensic examination is the determination of the type and model of firearms based on the class characteristics of these cartridge cases. A firearm examiner evaluates the class characteristics on the basis of their knowledge and experience, and by referring to collections of cartridge cases representing class characteristics of different firearms, special databases and reference books. However, this process is highly subjective. The novelty of this research is in developing objective methods of firearms determination by applying a machine learning approach. In this study, several Convolutional Neural Networks from Keras programming package were trained to determine the type/model of a firearm based on the class characteristics observed on cartridge cases from seven different categories of firearms. The prediction accuracies received by this method range from 71 to 81 percent for models based on different Convolutional Neural Networks, while using an ensemble of the machine learning models increased the accuracy to 88 %. The research demonstrates the efficacy of machine learning in enhancing accuracy and reducing subjectivity in firearm identification, highlighting its significant potential in forensic science applications.
    Language English
    Publishing date 2024-04-08
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 424042-x
    ISSN 1872-6283 ; 0379-0738
    ISSN (online) 1872-6283
    ISSN 0379-0738
    DOI 10.1016/j.forsciint.2024.112021
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    Zs.B 1104: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  4. Article: CIS: compound importance sampling method for protein-DNA binding site p-value estimation.

    Barash, Y / Elidan, G / Kaplan, T / Friedman, N

    Bioinformatics (Oxford, England)

    2005  Volume 21, Issue 5, Page(s) 596–600

    Abstract: ... a challenge.: Results: We present a general, accurate and efficient method for computing p-values ...

    Abstract Motivation: A key aspect of transcriptional regulation is the binding of transcription factors to sequence-specific binding sites that allow them to modulate the expression of nearby genes. Given models of such binding sites, one can scan regulatory regions for putative binding sites and construct a genome-wide regulatory network. In such genome-wide scans, it is crucial to control the amount of false positive predictions. Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge.
    Results: We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data.
    Availability: The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http://compbio.cs.huji.ac.il/CIS/ CONTACT: nir@cs.huji.ac.il.
    MeSH term(s) Algorithms ; Binding Sites ; DNA/chemistry ; DNA-Binding Proteins/chemistry ; Data Interpretation, Statistical ; Models, Biological ; Models, Chemical ; Models, Statistical ; Protein Binding ; Sample Size ; Sequence Analysis, DNA/methods ; Software ; Transcription Factors/chemistry
    Chemical Substances DNA-Binding Proteins ; Transcription Factors ; DNA (9007-49-2)
    Language English
    Publishing date 2005-03-01
    Publishing country England
    Document type Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4803
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/bti041
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    Zs.A 2374: Show issues Location:
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  5. Article ; Online: Effect of magnet strength on fetal brain biometry - a single-center retrospective MRI-based cohort study.

    Shrot, Shai / Hadi, Efrat / Barash, Yiftach / Hoffmann, Chen

    Neuroradiology

    2023  Volume 65, Issue 10, Page(s) 1517–1525

    Abstract: ... compared to the 1.5 T scanner (54.6th-centile, vs. 39.0th-centile, p < 0.001); less significant differences ... were found in vermis width centiles (46.9th-centile vs. 37.5th-centile, p = 0.03). Fronto-occipital ... diameter was higher in 1.5 T than in the 3.0 T scanner (66.0th-centile vs. 61.8th-centile, p = 0.02 ...

    Abstract Purpose: Abnormal fetal brain measurements might affect clinical management and parental counseling. The effect of between-field-strength differences was not evaluated in quantitative fetal brain imaging until now. Our study aimed to compare fetal brain biometry measurements in 3.0 T with 1.5 T scanners.
    Methods: A retrospective cohort of 1150 low-risk fetuses scanned between 2012 and 2021, with apparently normal brain anatomy, were retrospectively evaluated for biometric measurements. The cohort included 1.5 T (442 fetuses) and 3.0 T scans (708 fetuses) of populations with comparable characteristics in the same tertiary medical center. Manually measured biometry included bi-parietal, fronto-occipital and trans-cerebellar diameters, length of the corpus-callosum, vermis height, and width. Measurements were then converted to centiles based on previously reported biometric reference charts. The 1.5 T centiles were compared with the 3.0 T centiles.
    Results: No significant differences between centiles of bi-parietal diameter, trans-cerebellar diameter, or length of the corpus callosum between 1.5 T and 3.0 T scanners were found. Small absolute differences were found in the vermis height, with higher centiles in the 3.0 T, compared to the 1.5 T scanner (54.6th-centile, vs. 39.0th-centile, p < 0.001); less significant differences were found in vermis width centiles (46.9th-centile vs. 37.5th-centile, p = 0.03). Fronto-occipital diameter was higher in 1.5 T than in the 3.0 T scanner (66.0th-centile vs. 61.8th-centile, p = 0.02).
    Conclusions: The increasing use of 3.0 T MRI for fetal imaging poses a potential bias when using 1.5 T-based charts. We elucidate those biometric measurements are comparable, with relatively small between-field-strength differences, when using manual biometric measurements. Small inter-magnet differences can be related to higher spatial resolution with 3 T scanners and may be substantial when evaluating small brain structures, such as the vermis.
    MeSH term(s) Female ; Humans ; Retrospective Studies ; Cohort Studies ; Magnets ; Magnetic Resonance Imaging/methods ; Brain/diagnostic imaging ; Brain/anatomy & histology ; Biometry/methods
    Language English
    Publishing date 2023-07-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 123305-1
    ISSN 1432-1920 ; 0028-3940
    ISSN (online) 1432-1920
    ISSN 0028-3940
    DOI 10.1007/s00234-023-03193-y
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    Zs.A 658: Show issues Location:
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  6. Article ; Online: Machine learning applications in forensic DNA profiling: A critical review.

    Barash, Mark / McNevin, Dennis / Fedorenko, Vladimir / Giverts, Pavel

    Forensic science international. Genetics

    2023  Volume 69, Page(s) 102994

    Abstract: Machine learning (ML) is a range of powerful computational algorithms capable of generating predictive models via intelligent autonomous analysis of relatively large and often unstructured data. ML has become an integral part of our daily lives with a ... ...

    Abstract Machine learning (ML) is a range of powerful computational algorithms capable of generating predictive models via intelligent autonomous analysis of relatively large and often unstructured data. ML has become an integral part of our daily lives with a plethora of applications, including web, business, automotive industry, clinical diagnostics, scientific research, and more recently, forensic science. In the field of forensic DNA, the manual analysis of complex data can be challenging, time-consuming, and error-prone. The integration of novel ML-based methods may aid in streamlining this process while maintaining the high accuracy and reproducibility required for forensic tools. Due to the relative novelty of such applications, the forensic community is largely unaware of ML capabilities and limitations. Furthermore, computer science and ML professionals are often unfamiliar with the forensic science field and its specific requirements. This manuscript offers a brief introduction to the capabilities of machine learning methods and their applications in the context of forensic DNA analysis and offers a critical review of the current literature in this rapidly developing field.
    MeSH term(s) Humans ; DNA Fingerprinting ; Reproducibility of Results ; Forensic Sciences ; Machine Learning ; DNA/genetics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-12-01
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2493339-9
    ISSN 1878-0326 ; 1872-4973
    ISSN (online) 1878-0326
    ISSN 1872-4973
    DOI 10.1016/j.fsigen.2023.102994
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    Zs.A 6764: Show issues Location:
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  7. Book: Revolutionary biology

    Barash, David P.

    the new, gene-centered view of life

    2001  

    Author's details David P. Barash
    Language English
    Size VII, 213 S.
    Publisher Transaction Publ
    Publishing place New Brunswick, NJ u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT012974929
    ISBN 0-7658-0067-5 ; 978-0-7658-0067-1
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2001 A 3489 order for loan Magazin

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  8. Article ; Online: Novel Calcium-Sensing Receptor (CASR) Mutation in a Family with Autosomal Dominant Hypocalcemia Type 1 (ADH1): Genetic Study over Three Generations and Clinical Characteristics.

    Zung, Amnon / Barash, Galia / Banne, Ehud / Levine, Michael A

    Hormone research in paediatrics

    2023  Volume 96, Issue 5, Page(s) 473–482

    Abstract: ... cells transfected with wild type or mutant cDNAs demonstrated that p.Ile139Thr substitution led ... EC50 of 0.88 ± 0.02 mM vs. 1.1 ± 0.23 mM, respectively, p < 0.005). Clinical ...

    Abstract Introduction: Activating mutation of the calcium-sensing receptor gene (CASR) reduces parathyroid hormone secretion and renal tubular reabsorption of calcium, defined as autosomal dominant hypocalcemia type 1 (ADH1). Patients with ADH1 may present with hypocalcemia-induced seizures. Calcitriol and calcium supplementation in symptomatic patients may exacerbate hypercalciuria, leading to nephrocalcinosis, nephrolithiasis, and compromised renal function.
    Methods: We report on a family with seven members over three generations with ADH1 due to a novel heterozygous mutation in exon 4 of CASR: c.416T>C.
    Results: This mutation leads to substitution of isoleucine with threonine in the ligand-binding domain of CASR. HEK293T cells transfected with wild type or mutant cDNAs demonstrated that p.Ile139Thr substitution led to increased sensitivity of the CASR to activation by extracellular calcium relative to the wild-type CASR (EC50 of 0.88 ± 0.02 m<sc>M</sc> vs. 1.1 ± 0.23 m<sc>M</sc>, respectively, p < 0.005). Clinical characteristics included seizures (2 patients), nephrocalcinosis and nephrolithiasis (3 patients), and early lens opacity (2 patients). In 3 of the patients, serum calcium and urinary calcium-to-creatinine ratio levels obtained simultaneously over 49 patient-years were highly correlated. Using the age-specific maximal-normal levels of calcium-to-creatinine ratio in the correlation equation, we obtained age-adjusted serum calcium levels that are high enough to reduce hypocalcemia-induced seizures and low enough to reduce hypercalciuria.
    Conclusion: We report on a novel CASR mutation in a three-generation kindred. Comprehensive clinical data enabled us to suggest age-specific upper limit of serum calcium levels, considering the association between serum calcium and renal calcium excretion.
    MeSH term(s) Humans ; Hypocalcemia/genetics ; Receptors, Calcium-Sensing/genetics ; Calcium ; Hypercalciuria/genetics ; Nephrocalcinosis ; Creatinine ; HEK293 Cells ; Mutation ; Nephrolithiasis ; Seizures
    Chemical Substances Receptors, Calcium-Sensing ; Calcium (SY7Q814VUP) ; Creatinine (AYI8EX34EU) ; CASR protein, human
    Language English
    Publishing date 2023-02-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2537278-6
    ISSN 1663-2826 ; 1663-2818
    ISSN (online) 1663-2826
    ISSN 1663-2818
    DOI 10.1159/000529833
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    Zs.A 414: Show issues Location:
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  9. Article ; Online: A 10-year comparison of short versus long-term court-ordered psychiatric hospitalization: a follow-up study.

    Argo, Daniel / Daibas, Khaled / Barash, Igor / Abramowitz, Moshe Z

    Israel journal of health policy research

    2023  Volume 12, Issue 1, Page(s) 14

    Abstract: ... term hospitalizations for reducing instances of re-hospitalization (p = 0.889) and recidivism (p = 0.54 ...

    Abstract Background: The Israel Mental Health Act of 1991 stipulates a process for court-ordered involuntary psychiatric hospitalization. As in many Western countries, this process is initiated when an individual is deemed "not criminally responsible by reason of mental disorder (NCR-MD)" or "incompetent to stand trial (IST)." A patient thus hospitalized may be discharged by the district psychiatric committee (DPC). The decision rendered by the DPC is guided by an amendment to the Mental Health Act that states that the length of the hospitalization should be in accordance with the maximum time of incarceration associated with the alleged crime. Little empirical research has been devoted to the psychiatric, medical, and social outcome of short versus long-term hospitalization under court order.
    Methods: In our study we examined the outcomes of court-ordered criminal commitments over a 10-year period (2005-2015) at the Jerusalem Mental Health Center with a catchment area of 1.5 million. We found 136 cases (between the ages of 18 and 60) of criminal commitments during that period and used the average length of hospitalization, 205 days, as a cutoff point between short and long stays. We compared the outcomes of short and long hospitalizations of discharged patients using a follow-up phone survey (at least 7 years post-discharge) and data extracted from the Israel National Register to include recidivism, patient satisfaction and trust in the system, readmission, and demise.
    Results: We found no statistically significant difference between short-term and long-term hospitalizations for reducing instances of re-hospitalization (p = 0.889) and recidivism (p = 0.54), although there was a slight trend toward short-term hospitalization vis-à-vis reduced recidivism. We did not find a statistical difference in mortality or incidents of suicide between the two groups, but the absolute numbers are higher than expected in both of them. Moreover, our survey showed that short-term hospitalization inspired more trust in the legal process (conduct of the DPC), in pharmacological treatment satisfaction, and in understanding the NCR-MD as a step toward avoiding future hospitalization and that it resulted in a higher level of patient satisfaction.
    Conclusions: The results we present show that as far as recidivism and readmission are concerned, there is no evidence to suggest that there is an advantage to long-term hospitalization. Although there may be unmeasured variables not investigated in the present study that might have contributed to the discrepancy between long- and short-term hospitalization, we believe that longer hospitalizations may not serve the intended treatment purpose. Additionally, the high cost of long-term hospitalization and overcrowded wards are obviously major practical drawbacks. The impact of the clinical outcomes should be reflected in medico-legal legislation and in court-ordered hospitalization in particular.
    MeSH term(s) Humans ; Infant, Newborn ; Infant ; Follow-Up Studies ; Patient Discharge ; Aftercare ; Israel ; Length of Stay
    Language English
    Publishing date 2023-04-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2657655-7
    ISSN 2045-4015 ; 2045-4015
    ISSN (online) 2045-4015
    ISSN 2045-4015
    DOI 10.1186/s13584-023-00561-0
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  10. Article: Comparative sequence analysis of pPATH pathogenicity plasmids in

    Geraffi, Naama / Gupta, Priya / Wagner, Naama / Barash, Isaac / Pupko, Tal / Sessa, Guido

    Frontiers in plant science

    2023  Volume 14, Page(s) 1198160

    Abstract: Acquisition of the pathogenicity plasmid pPATH that encodes a type III secretion system (T3SS) and effectors (T3Es) has likely led to the transition of a non-pathogenic bacterium into the tumorigenic ... ...

    Abstract Acquisition of the pathogenicity plasmid pPATH that encodes a type III secretion system (T3SS) and effectors (T3Es) has likely led to the transition of a non-pathogenic bacterium into the tumorigenic pathogen
    Language English
    Publishing date 2023-07-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1198160
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