gebhart/patrepeval huggingface dataset:
How to Professionally Develop Reusable Scientific Software—And When Not To (2018)

A critical challenge in scientific computing is balancing developing high-quality software with the need for immediate scientific progress. We present a flexible approach that emphasizes writing specialized code that is refactored only when future immediate scientific goals demand it. Our lazy refactoring technique, which calls for code with clearly defined interfaces and sharply delimited scopes to maximize reuse and integrability, helps reduce total development time and accelerates the production of scientific results. We offer guidelines for how to implement such code, as well as criteria to aid in the evaluation of existing tools. To demonstrate their application, we showcase the development progression of tools for particle simulations originating from the Glotzer Group at the University of Michigan. We emphasize the evolution of these tools into a loosely integrated software stack of highly reusable software that can be maintained to ensure the long-term stability of established research workflows.
Compliance of 2012/13 Combat Ration Packs to the Recommended Nutritional Criteria (2014)

Abstract : DSTO has evaluated the nutrient content of 2012/13 Combat Ration One Man (CR1M), Patrol Ration One Man (PR1M) and Combat Ration Five Man (CR5M) against the Recommended Nutritional Criteria (RNC) for Combat Ration Packs (CRP). RNC ensure that soldiers are provided with their daily nutrient requirements when rationed on CRP. The evaluation was based primarily on analytical testing of samples of CRP components. The macronutrient and energy requirements generally met requirements. Compliance with the RNC for vitamins and minerals was better for CR1M and CR5M than for PR1M. The positive results for the 2012/13 CR1M in comparison to the 2008/09 CR1M, indicates that efforts to improve CRP have been effective.
Distribution and Rate of Movement of the Curtovirus Beet mild curly top virus (Family Geminiviridae) in the Beet Leafhopper (2003)

ABSTRACT A polymerase chain reaction (PCR)-based method for the detection of the curtovirus Beet mild curly top virus (BMCTV, previously named the Worland strain of Beet curly top virus) was developed and used to investigate the BMCTV-beet leafhopper interaction. Using PCR and a BMCTV-specific primer pair, an approximately 1.1-kb BMCTV DNA fragment was amplified from adult leafhoppers and from the organs involved in circulative transmission: the digestive tract, hemolymph, and salivary glands. The temporal distribution of BMCTV in the leafhopper was determined using insects given acquisition access periods (AAPs) ranging from 1 to 48 h on BMCTV-infected shepherd's purse plants. BMCTV was detected in the digestive tract after all AAPs, in the hemolymph after AAPs of 3 h or greater, and in the salivary glands after AAPs of 4 h or greater. The amount of virus detected in the hemolymph and salivary glands increased with AAP length. The virus persisted for up to 30 days in leafhoppers (given a 3-day AAP on BMCTV-infected plants) maintained on corn plants, a nonhost for BMCTV, but transovarial transmission was not detected. These results are consistent with a persistent but nonpropagative mode of circulative transmission.
Abstract 89: Mitochondrial Protein Acetylation in Aged Hearts in the Context of Ischemia-Reperfusion Injury (2014)

Introduction: SIRT3 deficiency leads to increased mitochondrial acetylation, and enhances sensitivity of the heart to stress. Recently we demonstrated that a worse outcome of ischemia-reperfusion (IR) injury in aged hearts was associated with increased protein acetylation. The aim of this study was to investigate the mechanism of acetylation and the identity of acetylated targets in aged hearts in the context of IR injury. Methods: Mitochondria were isolated from WT adult (7 mo.), SIRT3 +/- adult (7 mo.) and WT aged (18 mo.) hearts. SIRT3 protein expression and identification of acetylated proteins from SIRT3 +/- adult and WT aged samples were investigated using proteomics (2D gel, western blot, peptide mass fingerprinting). Results: Mitochondrial acetylome analysis revealed that many hyperacetylated patterns were identical between adult SIRT3 +/- and aged WT hearts, suggesting that increased protein acetylation in the aged WT heart might be due to SIRT3 inhibition. Several targets were indentified, including complex I NADH dehydrogenase flavoprotein 1, which is known to interact with SIRT3. In this regard, we demonstrated that respiratory complex I (CxI) activity was significantly inhibited in both SIRT3 +/- adult and WT aged hearts. Analysis of SIRT3 protein revealed that negatively charged species of SIRT3 (relative to the bulk SIRT3 population), were lost in aged hearts. These alterations suggest post-translational modification of SIRT3 which may lead to loss of its deacetylase activity. Alternatively, we found that upregulation of the mitochondrial acetyltransferase GCN5L1 in aged hearts (examined by western blot) may also contribute to enhanced protein acetylation. Conclusions: These data support a connection between SIRT3 downregulation, mitochondrial protein acetylation, and exacerbation of IR injury in aging hearts. Furthermore, it is known that functional CxI is required for several modes of cardioprotection suggesting that downregulation of CxI in SIRT3 +/- or WT aged hearts may underlie their poor recovery from IR injury.
Environmental robustness in speech recognition using physiologically-motivated signal processing (1993)

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13 Chapter 1 Introduction 14 Chapter 2 The SPHINX Speech Recognition System 18 2.1. Front-End Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.2. Vector Quantization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.3. Discrete Hidden Markov Model . . . . . . . . . . . . . . . . . . . . . . . . . 20 Chapter 3 Signal Processing Issues in Environmental Robustness 21 3.1. Sources of Degradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 3.1.1 Additive Noise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 3.1.2 Linear Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 3.1.3 Other Effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 3.2. Solutions to the Environmental Robus...
Evaluating the validity of anger regulation problems, interpersonal style, and disturbed mental state for predicting inpatient violence (2006)

Research has been conducted to try to identify risk factors to help predict which patients will be violent during psychiatric hospitalization. Despite the relatively large amount of research conducted, it is difficult to draw any firm conclusions, as the studies vary considerably in study design, methods used, and choice of outcome measures. Studies also tend to focus on risk prediction, even though risk management is the primary aim of clinical practice in mental health services and few studies have focused on a theoretical basis for understanding violence. This study assessed the predictive validity of brief assessment scales in a sample of 94 forensic inpatients who had been inpatient for a median of 521 days, to test the hypotheses that anger regulation problems, interpersonal style, and disturbed mental state would be linked to increased violence risk in a forensic hospital during a hospital stay. The outcome variables for this study were physical violence against another and/or clear threats of physical violence. The results of this study provide support for the hypotheses, and this remained the case after controlling for age, gender, length of stay, and presence of major mental disorder. The findings should not only assist clinicians with assessment and management of risk but also support the reconceptualizing of risk prediction research to reflect the task of clinical risk management.
Personalised-adaptive learning - an operational framework for developing competency-based curricula in computer information technology (2016)

In this paper, we explore the intersection of grounded theory in cognition and learning with the operational frameworks needed to develop and evaluate adaptive learning systems. As a test case, we studied an online personalised competency-based CIT curriculum at Northern Arizona University (Flagstaff, Arizona, USA). Our approach focused on strategies for adding adaptive learning capacities to an extant learning management system, with particular attention to cost-effective yet evidence-based approaches for improving learning outcomes. We designed elements that would enhance feedback and remediation for students, which required developing software engines that could integrate data collection and analysis. Such capacities are essential to drive evidence-based educational practices for CIT undergraduate and graduate programmes. Research led to a conceptual model and the operational facets for personalised-adaptive learning CIT educational environments. The conceptual and operational model described herein is called SIGNAL CIT Education - Serial Integration of Guiding Nodes for Adaptive Learning in CIT Education.
Microenvironment of histidine 12 in ribonuclease-S as detected by carbon-13 nuclear magnetic resonance (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicroenvironment of histidine 12 in ribonuclease-S as detected by carbon-13 nuclear magnetic resonanceIrwin M. Chaiken, Jack S. Cohen, and Edward A. SokoloskiCite this: J. Am. Chem. Soc. 1974, 96, 14, 4703–4705Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://pubs.acs.org/doi/10.1021/ja00821a073https://doi.org/10.1021/ja00821a073research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effects of temperature cycling on the optical strength of NaCl (1981)

We report a technique for increasing the laser-induced breakdown threshold in NaCl. Single-crystal NaCl was heated to near melting and rapidly quenched. This treatment resulted in a factor of 4.6 increase in the laser-induced damage threshold of the NaCl.
Hydrogen effect on characteristics of the resistive switching memory (2012)

Hydrogen anneal effects on reproducibility of the switching voltages for a resistive switching memory using anodic porous alumina have been investigated. The hydrogen anneal made the reproducibility worse.
Insights into the Mechanism of Anodic N–N Bond Formation by Dehydrogenative Coupling (2017)

The electrochemical synthesis of pyrazolidine-3,5-diones and benzoxazoles by N-N bond formation and C,O linkage, respectively, represents an easy access to medicinally relevant structures. Electrochemistry as a key technology ensures a safe and sustainable approach. We gained insights in the mechanism of these reactions by combining cyclovoltammetric and synthetic studies. The electron-transfer behavior of anilides and dianilides was studied and led to the following conclusion: The N-N bond formation involves a diradical as intermediate, whereas the benzoxazole formation is based on a cationic mechanism. Besides these studies, we developed a synthetic route to mixed dianilides as starting materials for the N-N coupling. The compatibility with valuable functionalities like triflates and mesylates for follow-up reactions as well as the comparison of different electrochemical set-ups also enhanced the applicability of this method.
Bridging Validation and Automatic Test Equipment (ATE) Environment (2012)

For getting high quality complex SoCs in market well in time requires many cross functional teams to work in tandem. One of the areas which we are focusing in this paper is collaboration between Validation and ATE teams. Validation needs to give production functional patterns to ATE to qualify the chip in mass production. These tests may be speed hunted patterns for Powerpc core or complex pattern for various IPs. Porting of validation testcases to ATE is a significant task and requires Logic Analyzer to capture signals. This causes significant delay in generating production ATE patterns. In this paper, we propose a new methodology where using scripts we can convert a validation test to ATE compatible testcase. One of the main advantage of this flow is that for pattern generation, there is no need to run the testcase either in simulation/emulation or to capture signals using Logic Analyzer. This flow also brings in a lot of debug capabilities and same test can be run across emulation, simulation, ATE and validation board. The new approach helps customer debug where customer failing scenarios can be converted into ATE patterns in matter of seconds.
Antidepressant fluorinated prothiadene derivatives: 9-Fluoro and 2,9-difluoro derivative of 11-(3-dimethylaminopropylidene)-6,11-dihydrodibenzo[b,e]thiepin (1982)

6-Fluorophthalide ( IV ), obtained from 6-aminophthalide by the Schiemann method, was transformed by reactions with potassium salts of thiophenol and 4-fluorothiophenol and 4-fluorothiophenol to the acid V and VI . Cyclization with polyphosphoric acid gave 9-fluoro- and 2,9-difluorodibenzo[ b,e ] thiepin-11(6 H )-one ( VII, VIII ) which were treated with 3-dimethylaminopropylmagnesium chloride and afforded the tertiary alcohols IX and X . Dehydration by heating with dilute hydrochloric acid resulted in the title compounds II and III whose IR spectra indicated the E -configuration. Both compounds showed properties of tricyclic antidepressants being, however, less active than prothiadene ( I ) in the tests for the antireserpine activity.
Self-aligned and shielded-RESURF LDMOS for dense 20 V power IC's (2003)

A self-aligned 20 V logic-level n-channel LDMOS has been integrated in a 0.6 /spl mu/m BiCMOS process, using a LATID (large angle tilted implementation drain) boron backgate implantation combined with co-implanted arsenic as a low-ohmic link under the spacer. In addition, a shielded RESURF LDMOS is reported for use as a low-side transistor in power converters, suited for 20 V in VLSI with a single thin gate oxide. This transistor suppresses parasitic injection in the substrate and uses a buried p on buried n/sup +/ layer.
Delayed Myocardial Infarction Associated With Rituximab Infusion (2015)

To report a case of delayed myocardial infraction after rituximab infusion. A 52-year-old woman with history of refractory idiopathic thrombocytopenic purpura had hypertension, seizure, and mild coronary artery disease and received rituximab; after 24 hours, she returned back with chest pain, nausea, and vomiting. Her electrocardiogram showed a ST-elevation in the II, III, aVF, and aVR lead and ST depression in I and aVL lead; after another complementary test, the myocardial infraction was confirmed. The patient was sent to the intensive care unit, and after 8-day hospitalization, she was discharged. Based on the Naranjo Probability Scale, the likelihood of rituximab-induced acute myocardial infarction in this case was probable. Rituximab is generally well tolerated; however, cardiovascular effects of this drug can be fatal. The side effects usually occur during or a short time after infusion; this case demonstrated that rituximab side effects may occur with delay. This case demonstrates, although a rare phenomenon, myocardial infraction may occur after 24 hours and clinicians should be aware of this fatal effect even after a period of time in patients receiving rituximab, especially in patients with history of coronary artery disease.
Design of Axial Blood Pumps for Patients With Dysfunctional Fontan Physiology: Computational Studies and Performance Testing (2015)

Limited treatment options for patients having dysfunctional single ventricle physiology motivate the necessity for alternative therapeutic options. To address this unmet need, we are developing a collapsible axial flow blood pump. This study investigated the impact of geometric simplicity to facilitate percutaneous placement and maintain optimal performance. Three new pump designs were numerically evaluated. A transient simulation explored the impact of respiration on blood flow conditions over the entire respiratory cycle. Prototype testing of the top performing pump design was completed. The top performing Rec design generated the highest pressure rise range of 2-38 mm Hg for flow rates of 1-4 L/min at 4000-7000 RPM, exceeding the performance of the other two configurations by more than 26%. The blood damage indices for the new pump designs were determined to be below 0.5% and predicted hemolysis levels remained low at less than 7 × 10(-5) g/100 L. Prototype testing of the Rec design confirmed numerical predictions to within an average of approximately 22%. These findings demonstrate that the pumps are reasonably versatile in operational ability, meet pressure-flow requirements to support Fontan patients, and are expected to have low levels of blood trauma.
Report from the CVOT Summit 2020: new cardiovascular and renal outcomes (2021)

Abstract The 6th Cardiovascular Outcome Trial (CVOT) Summit “Cardiovascular and Renal Outcomes 2020” was the first to be held virtually on October 29–30, 2020. As in previous years, this summit served as reference meeting for in-depth discussions on the topic of recently completed and presented major outcome trials. This year, focus was placed on the outcomes of VERTIS-CV, EMPEROR-Reduced, DAPA-CKD, and FIDELIO-DKD. Trial implications for diabetes management and the impact on new treatment algorithms were highlighted for diabetologists, cardiologists, endocrinologists, nephrologists, and general practitioners. Discussion evolved from major outcome trials using SGLT-2 inhibitors for treatment and prevention of heart failure and chronic kidney disease in people with and without diabetes, to additional therapy options for chronic kidney disease with a novel mineralocorticoid receptor antagonist. Furthermore, challenges in diabetes management like COVID-19 and obesity, as well as novel treatment strategies and guidelines, were discussed. The 7th Cardiovascular Outcome Trial Summit will be held virtually on November, 18–19, 2021 ( http://www.cvot.org ).
ChemInform Abstract: Synthesis and Pharmacological Evaluation of Novel N‐Alkyl/Aryl Substituted Thiazolidinone Arecoline Analogues as Muscarinic Receptor 1 Agonist in Alzheimer′s Dementia Models. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Circulating Phylotypes of White Spot Syndrome Virus in Bangladesh and Their Virulence (2022)

White Spot Syndrome Virus (WSSV) has emerged as one of the most prevalent and lethal viruses globally and infects both shrimps and crabs in the aquatic environment. This study aimed to investigate the occurrence of WSSV in different ghers of Bangladesh and the virulence of the circulating phylotypes. We collected 360 shrimp (<i>Penaeus monodon</i>) and 120 crab (<i>Scylla</i> sp.) samples from the south-east (Cox's Bazar) and south-west (Satkhira) coastal regions of Bangladesh. The VP28 gene-specific PCR assays and sequencing revealed statistically significant (<i>p</i> < 0.05, Kruskal-Wallis test) differences in the prevalence of WSSV in shrimps and crabs between the study areas (Cox's Bazar and Satkhira) and over the study periods (2017-2019). The mean Log load of WSSV varied from 8.40 (Cox's Bazar) to 10.48 (Satkhira) per gram of tissue. The mean values for salinity, dissolved oxygen, temperature and pH were 14.71 ± 0.76 ppt, 3.7 ± 0.1 ppm, 34.11 ± 0.38 °C and 8.23 ± 0.38, respectively, in the WSSV-positive ghers. The VP28 gene-based phylogenetic analysis showed an amino-acid substitution (E→G) at the 167th position in the isolates from Cox's Bazar (referred to as phylotype BD2) compared to the globally circulating one (BD1). Shrimp PL artificially challenged with BD1 and BD2 phylotypes with filtrates of tissue containing 0.423 × 10<sup>9</sup> copies of WSSV per mL resulted in a median LT50 value of 73 h and 75 h, respectively. The in vivo trial showed higher mean Log WSSV copies (6.47 ± 2.07 per mg tissue) in BD1-challenged shrimp PL compared to BD2 (4.75 ± 0.35 per mg tissue). Crabs infected with BD1 and BD2 showed 100% mortality within 48 h and 62 h of challenge, respectively, with mean Log WSSV copies of 12.06 ± 0.48 and 9.95 ± 0.37 per gram tissue, respectively. Moreover, shrimp antimicrobial peptides (AMPs), penaeidin and lysozyme expression were lower in the BD1-challenged group compared to BD2 challenged shrimps. These results collectively demonstrated that relative virulence properties of WSSV based on mortality rate, viral load and expression of host immune genes in artificially infected shrimp PL could be affected by single aa substitution in VP28.
Supplementary Figure 1 from Galectin-3 Cleavage Alters Bone Remodeling: Different Outcomes in Breast and Prostate Cancer Skeletal Metastasis (2023)

&lt;p&gt;Gal-3 is involved in osteoclastogenesis in bone tumor microenvironment.&lt;/p&gt;
A shaped reflector design for the DirecTv direct broadcast satellite for the United States (2002)

A design for the DirecTv DBS (direct broadcast satellite) coverage of the United States using a single shaped reflector is presented. This design is interesting and challenging because of the high ratio of the area of the coverage to the area of the pencil beam obtained using an unshaped reflector (>40). For the initial multifeed study, a parabolic reflector with a diameter of 96" was considered. After a detailed trade-off study, a design with a 56-element feed array was chosen. For the shaped reflector approach, a diameter of 85" was chosen after an initial trade-off study. A sensitivity study using a 'potato-chip' distortion model was conducted.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>