gebhart/patrepeval huggingface dataset:
Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites (2019)

Organ-on-chip technology allowed the identification of specific human microbiome metabolites modulating EHEC pathogenesis. These identified metabolites are sufficient to increase susceptibility to EHEC in our human Colon Chip model and they contribute to species-specific tolerance. This work suggests that higher concentrations of these metabolites could be the reason for higher susceptibility to EHEC infection in certain human populations, such as children. Furthermore, this research lays the foundation for therapeutic-modulation of microbe products in order to prevent and treat human bacterial infection.
Experimental and modeling study of fission products and minor actinides extraction with N,N-dialkylamides (2016)

International audience
Hospital Preparedness and SARS (2004)

On May 23, 2003, Toronto experienced the second phase of a severe acute respiratory syndrome (SARS) outbreak. Ninety cases were confirmed, and >620 potential cases were managed. More than 9,000 persons had contact with confirmed or potential case-patients; many required quarantine. The main hospital involved during the second outbreak was North York General Hospital. We review this hospital's response to, and management of, this outbreak, including such factors as building preparation and engineering, personnel, departmental workload, policies and documentation, infection control, personal protective equipment, training and education, public health, management and administration, follow-up of SARS patients, and psychological and psychosocial management and research. We also make recommendations for other institutions to prepare for future outbreaks, regardless of their origin.
Giant anomalous Hall effect from spin-chirality scattering in a chiral magnet (2020)

The electrical Hall effect can be significantly enhanced through the interplay of the conduction electrons with magnetism, which is known as the anomalous Hall effect (AHE). Whereas the mechanism related to band topology has been intensively studied towards energy efficient electronics, those related to electron scattering have received limited attention. Here we report the observation of giant AHE of electron-scattering origin in a chiral magnet MnGe thin film. The Hall conductivity and Hall angle respectively reach 40,000 Ω-1cm-1 and 18 % in the ferromagnetic region, exceeding the conventional limits of AHE of intrinsic and extrinsic origins, respectively. A possible origin of the large AHE is attributed to a new type of skew-scattering via thermally-excited spin-clusters with scalar spin chirality, which is corroborated by the temperature-magnetic-field profile of the AHE being sensitive to the film-thickness or magneto-crystalline anisotropy. Our results may open up a new platform to explore giant AHE responses in various systems, including frustrated magnets and thin-film heterostructures.
Differences in Adiposity in Cushing Syndrome Caused byPRKAR1AMutations: Clues for the Role of Cyclic AMP Signaling in Obesity and Diagnostic Implications (2013)

Increased PKA signaling in PAT was associated with lower BMI in CS. Differences in fat distribution may contribute to phenotypic differences between patients with CS with and without PRKAR1A mutations. The observed differences are in agreement with the known roles of cAMP signaling in regulating adiposity, but this is the first time that germline defects of PKA are linked to variable obesity phenotypes in humans.
Pediatric cavernous sinus and superior ophthalmic vein thrombophlebitis complicated by peri-venous orbital abscesses (2022)

This case report describes a pediatric patient with bilateral cavernous sinus thrombosis who developed the rare complication of multiple peri-venous orbital abscesses despite appropriate treatment with antibiotics. The patient's complex clinical course highlights the importance of prompt repeat imaging and possible surgical intervention upon clinical changes, especially in patients with infections from the <i>Streptococcus milleri</i> group.
On the Normal Component of Centralized Frictionless Collision Sequences (2001)

A typical assumption for rigid body collisions with multiple impact points is that all collisions occur simultaneously and are synchronized in their compression/expansion behavior, a useful assumption given the microscopic time scale at which collisions occur. In the case in which collisions are dependent upon one another, however, there is interaction between and within compression and expansion phases. Instead of treating the collisions as separate consecutive impacts or by activating all constraints at the same time, a rule is presented that orders the collisions as a sequence of interacting events at a point in time to handle the normal component of the collisions.
The NIMA-family kinase Nek3 regulates microtubule acetylation in neurons (2009)

NIMA-related kinases (Neks) belong to a large family of Ser/Thr kinases that have critical roles in coordinating microtubule dynamics during ciliogenesis and mitotic progression. The Nek kinases are also expressed in neurons, whose axonal projections are, similarly to cilia, microtubule-abundant structures that extend from the cell body. We therefore investigated whether Nek kinases have additional, non-mitotic roles in neurons. We found that Nek3 influences neuronal morphogenesis and polarity through effects on microtubules. Nek3 is expressed in the cytoplasm and axons of neurons and is phosphorylated at Thr475 located in the C-terminal PEST domain, which regulates its catalytic activity. Although exogenous expression of wild-type or phosphomimic (T475D) Nek3 in cultured neurons has no discernible impact, expression of a phospho-defective mutant (T475A) or PEST-truncated Nek3 leads to distorted neuronal morphology with disturbed polarity and deacetylation of microtubules via HDAC6 in its kinase-dependent manner. Thus, the phosphorylation at Thr475 serves as a regulatory switch that alters Nek3 function. The deacetylation of microtubules in neurons by unphosphorylated Nek3 raises the possibility that it could have a role in disorders where axonal degeneration is an important component.
ChemInform Abstract: Synthesis of Optically Pure α‐Halo‐α′‐sulphinyl‐ketones. (1986)

Abstract Aus den Sulfoxiden (I) erhält man über die entsprechenden optisch reinen Carbanionen durch Kondensation mit den Halogencarbonsäureestern (II) die Addukte (III) in hohen Ausbeuten und optisch reiner Form.
Implementation of UTC-compliant Leap Seconds in Microsoft Windows (2019)

Regulations governing fairness in the financial markets mandate accuracy and traceability at all times, including during leap seconds. Leap seconds are difficult for computer systems to implement in accordance with the UTC definition for a variety of reasons. This paper discusses the implementation of UTC-compliant leap seconds in Microsoft Windows 10 October 2018 Update and Windows Server 2019, the adaptations we have put in place to address potential application compatibility issues, and demonstrates high accuracy time keeping when leap seconds roll over.
Cost Effective Developments for Fabrication of Titanium Components (2013)

The major reason that there is not more widespread use of titanium and its alloys is the high cost. In this paper, developments in one cost effective approach to fabrication of titanium components - powder metallurgy - will be discussed under various aspects of this technology. The aspects to be discussed are the blended elemental approach, pre-alloyed techniques, additive layer manufacturing, metal injection molding, spray deposition and microwave sintering. A brief review of a number of low cost powder production processes is also presented.
Host Directed Therapy for Chronic Tuberculosis via Intrapulmonary Delivery of Aerosolized Peptide Inhibitors Targeting the IL-10-STAT3 Pathway (2018)

Here we demonstrate that aerosols of host directed therapies [HDT] administered during a chronic Mycobacterium tuberculosis (Mtb) infection have bactericidal effect. The pulmonary bacterial load of C57BL/6 mice chronically infected with Mtb was reduced by 1.7 and 0.6 log<sub>10</sub>CFU after two weeks of treatment via aerosol delivery with ST3-H2A2, [a selective peptide inhibitor of the STAT3 N-terminal domain] or IL10R1-7 [selective peptide inhibitor for the IL-10Ra] respectively and when compared to control mice treated with IL10R1-14 [peptide inhibitor used as negative control] or untreated mice infected with Mtb. Accordingly, when compared to control mice, the bactericidal capacity in mice was enhanced upon treatment with peptide inhibitors ST3-H2A2 and IL10R1-7 as evidenced by higher pulmonary activities of nitric oxide synthase, NADPH oxidase and lysozyme enzymes and decreased arginase enzyme activity. This therapy also modulated important checkpoints [Bcl2, Beclin-1, Atg 5, bax] in the apoptosis-autophagy pathways. Thus, even in the absence of antibiotics, targeting of the host pulmonary IL-10-STAT3 pathway can significantly reduce the Mtb bacilli load in the lungs, modulate the host own bactericidal capacity and apoptosis and autophagy pathways. Our approach here also allows targeting checkpoints of the lungs to determine their specific contribution in pulmonary immunity or pathogenesis.
In-situ interfacial compatibilization via edge-sulfurated few layer graphene during the formation of crosslinked graphene-rubber nanocomposites (2022)

Herein, we report various physico-chemical approaches to probe the nature of the interface between few layers graphene (FLG) and carboxylated nitrile rubber (XNBR) nanocomposites prepared through efficient blending of XNBR latex with an aqueous dispersion of FLG. The extent of physical interaction between FLG and XNBR was investigated using Lorentz-Park and Cunneen-Russell models. The chemical interface between FLG and sulfur crosslinked XNBR was studied using model reactions between sulfur and graphene in presence of zinc 2-mercaptobenzothiazole (ZMBT). We propose that an edge sulfurated FLG is formed, which could chemically bond with XNBR during the vulcanization process. Density Functional Theory (DFT) was employed to unravel the mechanistic insights, which support this hypothesis and suggest a kinetically favorable sulfuration of both XNBR and FLG. The formation of a chemical bond between edge-FLG and XNBR through the proposed intermediacy of sulfurated FLG leads to the observed improvement in mechanical properties of the nanocomposites.
Instrumenting the Human into Safety 4.0 (2022)

Managing the workers’ health and safety faces many challenges due to the dependency on human interactions especially when it comes to human monitoring and detecting nonconformance. Conventionally, the input to HSE making decisions is collected from the worker himself or by an HSE officer making it mostly biased and hard to communicate. The team proposes a constant and continuous approach to objectively monitor the workers using machine vision capabilities along with smart decision-making tools to detect, recognize and classify human behaviors. The input of the system is coherent and effective while the output is unbiased, quantifiable, and communicable, the needed ingredients to integrate the human worker into Industry 4.0. The scope of this work focuses on the worker’s health and safety setting another building block in the Safety 4.0 vision. The proposed system consists of multiple integrated components including continuous video streaming devices, Machine vision components, computer logic for decision making, communication schemes, and locally implemented effectors. The system was tested on a simulated environment using a human factors simulation platform then was validated with actual environments with workers acting with HSE nonconformance while performing different tasks. The results show the system’s ability to recognize the human posture, speed, and throughput then compare it to the HSE guidelines. The results also show that the system was able to provide fast responses by giving warnings, reporting an incident to the management, or shutting the process down if an injury is recognized. Finally, the system generates data and reports that are ready to be transmitted onto the Internet of Things.
Hardware Trojans (2016)

Given the increasing complexity of modern electronics and the cost of fabrication, entities from around the globe have become more heavily involved in all phases of the electronics supply chain. In this environment, hardware Trojans (i.e., malicious modifications or inclusions made by untrusted third parties) pose major security concerns, especially for those integrated circuits (ICs) and systems used in critical applications and cyber infrastructure. While hardware Trojans have been explored significantly in academia over the last decade, there remains room for improvement. In this article, we examine the research on hardware Trojans from the last decade and attempt to capture the lessons learned. A comprehensive adversarial model taxonomy is introduced and used to examine the current state of the art. Then the past countermeasures and publication trends are categorized based on the adversarial model and topic. Through this analysis, we identify what has been covered and the important problems that are underinvestigated. We also identify the most critical lessons for those new to the field and suggest a roadmap for future hardware Trojan research.
3-Amino-pyrrolo[3,4-c]pyrazoles: A new class of CDK2 inhibitors. (2004)

2479 In the last few years the field of kinase inhibition has seen a constant surge of interest across different therapeutic areas. CDK2/cyclin A-E has been the subject of many research projects in the pharmaceutical industry. Several chemotypes have been described leading to potent inhibitors though only few of them have as yet progressed into a clinical stage. We have previously described 3-aminopyrazole inhibitors of CDK2/cyclin A-E. In an effort to explore related chemotypes which differently exploit the ATP kinase binding, we expanded a class of 3-Amino-1,4,5,6-tetrahydropyrrolo[4,3-c]pyrazoles. This scaffold, in contrast to the 3-aminopyrazoles, allows to easily direct substituents into the phosphate binding region of the ATP pocket of kinases. In this communication we describe the preliminary expansion and Structure-Activity Relationship of this class. From initial hits with moderate potency against both CDK2 and Aurora, we got to a series of compounds with submicromolar activity against both kinases. With an appropriate choice of substituents at R3 and R5 we obtained compounds with potent and selective CDK2/cyclin A activity in biochemical and cellular assays.
A Universal Hardware-Driven PVT and Layout-Aware Predictive Failure Analytics for SRAM (2015)

The impact of device variability, temperature, and technology CAD-based layout parasitics on low-voltage static random access memory (SRAM) yield is explored using a novel variability-aware statistical methodology. Threshold voltage, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> , mismatches for planar 22- and 14-nm FinFET SRAM transistors are characterized based on unique array-like structures for capturing process voltage and temperature (PVT) impact on variability. In general, the mismatches are shown to be a consistent and unique function of V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> , doping, and temperature across the two technologies. Stronger Vt mismatch impact is observed as a function of V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> and doping in the 22-nm technology, with higher mismatch recorded at lower temperatures. In the 14-nm technology, doping is found to have the strongest impact on V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> mismatch, and the mismatch increases with V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> despite the reduced drain induced barrier lowering effects. Similar to the 22-nm technology, the mismatch increases at lower temperatures. Front-end-of-the line capacitance effects are found to be more significant than back-end-of-the-line effects in 14-nm technologies, as opposed to planar technologies. Accurate parasitic capacitance modeling along with PVT-aware variability process variations for different 22-/14-nm cell arrangements are incorporated into a physics based statistical analysis methodology for accurate Vmin analysis. The yield analysis results are corroborated with hardware yield using 4-16-Mb inline SRAM macro monitors. The methodology is unique in the industry, gives insight into the technology-circuit interactions, and is able to effectively predict the SRAM yield bounds.
Ebola virus delta peptide is an enterotoxin (2022)

During the 2013-2016 West African (WA) Ebola virus (EBOV) outbreak, severe gastrointestinal symptoms were common in patients and associated with poor outcome. Delta peptide is a conserved product of post-translational processing of the abundant EBOV soluble glycoprotein (sGP). The murine ligated ileal loop model was used to demonstrate that delta peptide is a potent enterotoxin. Dramatic intestinal fluid accumulation follows injection of biologically relevant amounts of delta peptide into ileal loops, along with gross alteration of villous architecture and loss of goblet cells. Transcriptomic analyses show that delta peptide triggers damage response and cell survival pathways and downregulates expression of transporters and exchangers. Induction of diarrhea by delta peptide occurs via cellular damage and regulation of genes that encode proteins involved in fluid secretion. While distinct differences exist between the ileal loop murine model and EBOV infection in humans, these results suggest that delta peptide may contribute to EBOV-induced gastrointestinal pathology.
Recognition Of 3D Curves Based On Curvature And Torsion (1988)

Various range sensors are being used as part of a machine vision system to capture the surface of a 3D object. Significant structural changes on the surface, such as zero gaussian curvature contours, can be detected and regarded as 3D curves using differential geometry tools. In this paper, we present a technique for recognition of partially visible 3D curves which can be employed to identify 3D objects. A local/global represenation of a 3D curve is obtained by decomposing it into a number of invariant 3D curve segments. Based on curvature and torsion functions, feature vectors are assigned to the curve segments. A distance measure is then defined between two decomposed 3D curves using their corresponding feature vectors. The recognition of an occluded curve among known reference curves is achieved by obtaining the smallest distance measure. Experimental results on both simulated and real data are presented.
Kratom use as more than a “self-treatment” (2022)

<i>Background:</i> <i>Mitragyna speciosa</i> (kratom) is increasingly used in the United States for its pharmacological effects. Kratom's relative novelty makes for a dynamic situation, such that use motivations are not firmly established and may be changing. Investigators and clinicians require frequent updates on kratom trends.<i>Objectives:</i> To assess the current state of kratom-use initiation, sourcing, motivations, preference, conceptualizations, and perceived stigma, using survey responses from current and former users.<i>Methods:</i> Between April-May 2021 we recontacted 289 respondents who reported lifetime kratom use (on an unrelated survey) to answer kratom-specific questions.<i>Results:</i> The sample (N=129) was majority female (51.9%) and white (71.9%). Most (69.0%) reported first trying kratom after 2015. Mean age of use initiation (29.9 years) was older than for other substances, including opioids. Kratom ranked as a preferred substance by 48.5%. The strongest drug association with past-year kratom use was vaped nicotine (<i>OR=</i>3.31,95% CI 1.23-8.88). Use was less likely among those prescribed buprenorphine in the past year (<i>OR=</i>0.03, CI 0.01-0.28). Past-month cannabis use (<i>OR=</i>4.18,CI 1.80-9.72) had the strongest association with past-month kratom use. Over 40 use motivations were endorsed, many (but not all) supporting the "self-treatment" narrative of kratom use, including use as an opioid, alcohol, or stimulant substitute. Treatment shortfalls were associated with decisions to try kratom.<i>Conclusions:</i> Kratom use motivations are diversifying, with multiple factors driving use. As sales continue to increase, the public-health, clinical, and policy responses to kratom should be grounded in rigorous bench-to-bedside scientific research. Comprehensive study of kratom is currently lacking.
tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities (2014)

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.
The thorny complexities of visualization research for clinical settings: A case study from genomics (2023)

In this perspective article we discuss a certain type of research on visualization for bioinformatics data, namely, methods targeting clinical use. We argue that in this subarea additional complex challenges come into play, particularly so in genomics. We here describe four such challenge areas, elicited from a domain characterization effort in clinical genomics. We also list opportunities for visualization research to address clinical challenges in genomics that were uncovered in the case study. The findings are shown to have parallels with experiences from the diagnostic imaging domain.