gebhart/patrepeval huggingface dataset:
Review 1: Intestinal receptor of SARS-CoV-2 in inflamed IBD tissue is downregulated by HNF4A in ileum and upregulated by interferon regulating factors in colon (2020)

Study claims increased susceptibility of IBD patients to SARS-CoV-2 infection. Study lacks sufficient evidence to support the authors’ claims concerning the importance of IBD medication in COVID-19 risk management. Claims are not actionable except to prompt further research.
A roughness measure for 3D mesh visual masking (2007)

3D models are subject to a wide variety of processing operations such as compression, simplification or watermarking, which introduce slight geometric modifications on the shape. The main issue is to maximize the compression/simplification ratio or the watermark strength while minimizing these visual degradations. However few algorithms exploit the human visual system to hide these degradations, while perceptual attributes could be quite relevant for this task. Particularly, the Masking Effect defines the fact that a signal can be masked by the presence of another signal with similar frequency or orientation. In this context we introduce the notion of roughness for a 3D mesh, as a local measure of geometric noise on the surface. Indeed, a textured (or rough) region is able to hide geometric distortions much better than a smooth one. Our measure is based on curvature analysis on local windows of the mesh and is independent of the resolution/connectivity of the object. An application to Visual Masking is presented and discussed.
ChemInform Abstract: Synthesis and Adenosine Receptor Affinity of 7‐β‐D‐Ribofuranosylxanthine. (1998)

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.
Mixed reality for supporting office devices troubleshooting (2011)

In this paper we describe the Mixed Reality system that we are developing to facilitate a real-world application, that of collaborative remote troubleshooting of broken office devices. The architecture of the system is centered on a 3D virtual representation of the device augmented with status data of the actual device coming from its internal sensors. The purpose of this paper is to illustrate how this approach supports the interactions required by the remote collaborative troubleshooting activity whilst taking into account technical constraints that come from a real world application. We believe it constitutes an interesting opportunity for using Mixed Reality in this domain.
Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage (2021)

<i>Clostridioides difficile</i> is the leading cause of antibiotic-associated diarrhea and is capable of causing severe symptoms, such as pseudomembranous colitis and toxic megacolon. An unusual feature of <i>C. difficile</i> is the distinctive production of high levels of the antimicrobial compound <i>para</i>-cresol. <i>p</i>-Cresol production provides <i>C. difficile</i> with a competitive colonization advantage over gut commensal species, in particular, Gram-negative species. <i>p</i>-Cresol is produced by the conversion of <i>para</i>-hydroxyphenylacetic acid (<i>p</i>-HPA) <i>via</i> the actions of HpdBCA decarboxylase coded by the <i>hpdBCA</i> operon. Host cells and certain bacterial species produce <i>p</i>-HPA; however, the effects of <i>p</i>-HPA on the viability of <i>C. difficile</i> and other gut microbiota are unknown. Here we show that representative strains from all five <i>C. difficile</i> clades are able to produce <i>p</i>-cresol by two distinct mechanisms: (i) <i>via</i> fermentation of <i>p</i>-tyrosine and (ii) <i>via</i> uptake and turnover of exogenous <i>p</i>-HPA. We observed strain-specific differences in <i>p</i>-cresol production, resulting from differential efficiency of <i>p-</i>tyrosine fermentation; representatives of clade 3 (CD305) and clade 5 (M120) produced the highest levels of <i>p</i>-cresol <i>via</i> tyrosine metabolism, whereas the toxin A-/B+ isolate from clade 4 (M68) produced the lowest level of <i>p</i>-cresol. All five lineages share at least 97.3% homology across the <i>hpdBCA</i> operon, responsible for decarboxylation of <i>p</i>-HPA to <i>p</i>-cresol, suggesting that the limiting step in <i>p</i>-cresol production may result from tyrosine to <i>p</i>-HPA conversion. We identified that elevated intracellular <i>p</i>-HPA, modulated indirectly <i>via</i> CodY, controls <i>p</i>-cresol production <i>via</i> inducing the expression of HpdBCA decarboxylase ubiquitously in <i>C. difficile</i> populations. Efficient turnover of <i>p</i>-HPA is advantageous to <i>C. difficile</i> as <i>p</i>-HPA has a deleterious effect on the growth of <i>C. difficile</i> and other representative Gram-negative gut bacteria, transduced potentially by the disruption of membrane permeability and release of intracellular phosphate. This study provides insights into the importance of HpdBCA decarboxylase in <i>C. difficile</i> pathogenesis, both in terms of <i>p</i>-cresol production and detoxification of <i>p</i>-HPA, highlighting its importance to cell survival and as a highly specific therapeutic target for the inhibition of <i>p</i>-cresol production across <i>C. difficile</i> species.
Differentiable Programming of Chemical Reaction Networks (2023)

We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by nature. We study well-mixed single-chamber systems, as well as systems with multiple chambers separated by membranes, under mass-action kinetics. We demonstrate that differentiable optimisation, combined with proper regularisation, can discover non-trivial sparse reaction networks that can implement various sorts of oscillators and other chemical computing devices.
A design of single carrier based PHY for IEEE 802.15.3c standard (2007)

This paper proposes an air interface for ultra high-speed millimeter wave (60 GHz) systems which have been under standardization process at IEEE 802.15.3c: the proposed channel plan permits ease of portable device implementation employing the major crystal oscillator used in CDMA cellar phones. The proposed transmission modes offer much greater scalability, covering from several tens Mbps to over 4 Gbps. The proposed preamble employs Golay codes, providing sufficient robustness against wireless environment being subject to the characteristics of millimeter wave with reduced hardware complexity. Common mode is a novel technique to communicate with single carrier (SC) and OFDM camps with multi rates up to around 1.5 Gbps. This technique gives the proposed systems easy expandability from SC to OFDM or other SCs and vice versa.
Diabetes mellitus : a fundamental and clinical text (2004)

Thoroughly revised and updated, this Third Edition encompasses the most recent advances in molecular and cellular research and describes the newest therapeutic modalities for type 1 and type 2 diabetes mellitus. Chapters by leading experts integrate the latest basic science and clinical research on diabetes mellitus and its complications. The text is divided into ten major sections, including extensive sections on therapeutics, diabetes during pregnancy, and complications. New chapters cover stem cell therapy for type 1 diabetes; genetics and treatment of obesity; new therapies to promote insulin action; vasculopathy; islet cell protocols; triglycerides in muscle; hypoglycemia in the adult; and the Diabetes Prevention Program.
Mechanism of Fatal Chest Injury by Baseball Impact (1992)

This study describes the development of an animal model to characterize the mechanism of death by baseball impact of the chest in children. Sixteen anesthetized animals were subjected to midsternal, blunt chest trauma by a baseball accelerated to 95 mph (42.8 m/s). At this speed, death occurred by traumatic arrhythmia and apnea. The animals were divided into two groups: 10 were breathing spontaneously and six underwent controlled ventilation. All animals developing ventricular fibrillation as the initial arrhythmia died regardless of ventilatory status. Survival related to the use of ventilatory support. Four of the six (66.7%) ventilated animals survived, as opposed to two of 10 (20.0%) animals breathing spontaneously (χ2 = p < 0.06). Necropsy revealed minor myocardial contusions but none sufficient to cause death. The study has generated a reproducible model of pediatric cardiac arrest induced by high-speed baseball impact and emphasizes the role of ventricular fibrillation and adequate ventilatory support.
The Population Dynamics of Antibiotic Resistance in Staphylococcus aureus in Boston: A Return to Antibiotic Susceptibility (2017)

Methicillin resistant Staphylococcus aureus (MRSA) has been declining over the past decade, but changes in S. aureus overall and the implications for trends in antibiotic resistance remain unclear. We determine whether the decline in rates of infection by MRSA has been accompanied by changes in rates of infection by methicillin susceptible, penicillin resistant S. aureus (MSSA) and penicillin susceptible S. aureus (PSSA). We test if these dynamics are associated with specific genetic lineages and evaluate gains and losses of resistance at the strain level. We conducted a 15 year retrospective observational study at two tertiary care institutions in Boston, MA of 31,589 adult inpatients with S. aureus infections. Surveillance swabs and duplicate specimens were excluded. We also sequenced a sample of contemporary isolates (n = 180) obtained between January 2016 and July 2016. We determined changes in the annual rates of infection per 1,000 inpatient admissions by S. aureus subtype and in the annual mean antibiotic resistance by subtype. We performed phylogenetic analysis to generate a population structure and infer gain and loss of the genetic determinants of resistance. Of the 43,954 S. aureus infections over the study period, 21,779 were MRSA, 17,565 MSSA and 4,610 PSSA. After multivariate adjustment, annual rates of infection by S. aureus declined from to 2014 by 2.9% (95% confidence interval (CI), 1.6%–4.3%), attributable to an annual decline in MRSA of 9.1% (95% CI, 6.3%–11.9%) and in MSSA by 2.2% (95% CI, 0.4%–4.0%). PSSA increased over this time period by 4.6% (95% CI, 3.0%–6.3%) annually. Resistance in S. aureus decreased from 2000 to 2014 by 0.86 antibiotics (95% CI, 0.81–0.91). By phylogenetic inference, 5/35 MSSA and 2/20 PSSA isolates in the common MRSA lineages ST5/USA100 and ST8/USA300 arose from the loss of genes conferring resistance. At two large tertiary care centers in Boston, S. aureus infections have decreased in rate and have become more susceptible to antibiotics, with a rise in PSSA making penicillin an increasingly viable and important treatment option. All authors: No reported disclosures.
Chemistry of mycolactones, the causative toxins of Buruli ulcer (2011)

Buruli ulcer is a severe and devastating skin disease caused by Mycobacterium ulcerans infection, yet it is one of the most neglected diseases. The causative toxin, referred to as mycolactone A/B, was isolated and characterized as a polyketide-derived macrolide in 1999. The current status of the mycolactone chemistry is described, highlighting the stereochemistry assignment of mycolactone A/B; total synthesis; the structure determination of mycolactone congeners from the human pathogen M. ulcerans, the frog pathogen Mycobacterium liflandii, and the fish pathogen Mycobacterium marinum; the structural diversity in the mycolactone class of natural products; the highly sensitive detection/structure-analysis of mycolactones; and some biological activity.
A Synthesis of the Potent A2Selective Adenosine Agonist N6-[2-(3,5-Dimethoxyphenyl)-2-(2-Methylphenyl)Ethyl]Adenosine, and Its 5′-N-Ethyl Ribofuranuronamide Derivative (1989)

Abstract A detailed experimental procedure for the synthesis and resolution of 2-(3,5-dimethoxyphenyl)-2-(2-methylphenyl)ethylamine, and its conversion into the titled adenosine reference agonists is given.
MP34-03 AN OPEN-LABEL, NEOADJUVANT PHASE 2 CLINICAL TRIAL COMPARING THE EFFECTS OF AR INHIBITION WITH AND WITHOUT SRC OR MEK INHIBITION ON THE DEVELOPMENT OF EMT IN PROSTATE CANCER: AN OUTCOME REPORT (2019)

surrounding structures. The wound is closed with a series of purse string 2-0 Maxon sutures.
Tissue Formation and Vascularization in Anatomically Shaped Human Joint Condyle Ectopically in Vivo (2009)

Scale-up of bioengineered grafts toward clinical applications is a challenge in regenerative medicine. Here, we report tissue formation and vascularization of anatomically shaped human tibial condyles ectopically with a dimension of 20 x 15 x 15 mm(3). A composite of poly-epsilon-caprolactone and hydroxyapatite was fabricated using layer deposition of three-dimensional interlaid strands with interconnecting microchannels (400 microm) and seeded with human bone marrow stem cells (hMSCs) with or without osteogenic differentiation. An overlaying layer (1 mm deep) of poly(ethylene glycol)-based hydrogel encapsulating hMSCs or hMSC-derived chondrocytes was molded into anatomic shape and anchored into microchannels by gel infusion. After 6 weeks of subcutaneous implantation in athymic rats, hMSCs generated not only significantly more blood vessels, but also significantly larger-diameter vessels than hMSC-derived osteoblasts, although hMSC-derived osteoblasts yielded mineralized tissue in microchannels. Chondrocytes in safranin-O-positive glycosaminoglycan matrix were present in the cartilage layer seeded with hMSC-derived chondrogenic cells, although significantly more cells were present in the cartilage layer seeded with hMSCs than hMSC-derived chondrocytes. Together, MSCs elaborate substantially more angiogenesis, whereas their progenies yield corresponding differentiated tissue phenotypes. Scale up is probable by incorporating a combination of stem cells and their progenies in repeating modules of internal microchannels.
On-resonant balanced Steady-State Free Precession imaging at 9.4T (2016)

In this work, we explore the possibility of using the recently proposed highly undersampled 3D phase-cycled balanced Steady-State Free Precession (bSSFP) sequence trueCISS to generate on-resonant band-free bSSFP images at 9.4T. By applying the forward signal model, it is also possible to synthetically generate bSSFP images at higher flip angles, which would otherwise be impossible to acquire due to SAR limitations. Lastly, we show a maximum bSSFP signal intensity image of the brain using the trueCISS estimated parameter maps.
Novel Resveratrol-Based Aspirin Prodrugs: Synthesis, Metabolism, and Anticancer Activity (2015)

Regular aspirin use has been convincingly shown to reduce the risk of colorectal cancer. However, long-term use of aspirin leads to gastrotoxicity. Herein, we designed and synthesized a novel class of resveratrol-based aspirin prodrugs to simultaneously release aspirin and resveratrol to attenuate the side effects caused by aspirin. Prodrug RAH exerted enhanced anticancer activities which are better than a physical mixture of aspirin and resveratrol as well as each individually. Metabolism of RAH in mice showed that the majority of RAH is decomposed to release resveratrol and aspirin or salicylic acid either in the intestine or after absorption. Mechanistic studies demonstrate RAH inhibits cell cycle arrest through downregulation of cyclins and induces apoptosis by activation of caspase-3 in cancer cells. These findings highlighted the improved anticancer properties of resveratrol-based aspirin prodrugs. RAH may represent novel and safe alternatives of aspirin for the purpose of daily use in the future.
Detection of Cytopathic Bovine Viral Diarrhea Virus in the Ovaries of Cattle following Immunization with a Modified Live Bovine Viral Diarrhea Virus Vaccine (1998)

Economic loss from infection with bovine viral diarrhea virus (BVDV) is of worldwide concern. The unique pathogenesis and antigenic variability of BVDV have made this virus challenging to control. Vaccination programs are a major component of control and prevention strategies. Both killed and modified live vaccines are commercially available. Choice between killed and modified live vaccines is controversial. Of major concern is the safety of modified live vaccines. Little information is available on their tissue tropism and potential for causing pathology, especially with respect to the reproductive system. The objective of this study was to determine if BVDV could be detected in the ovary of cattle following immunization with a modified live BVDV vaccine. In 2 separate trials, 6 heifers and 4 mature cows were immunized with a modified live BVDV vaccine and ovaries were removed between 7 and 30 days postvaccination. Cytopathic BVDV was isolated from ovaries removed on days 8, 10, and 12. BVDV antigen was detected using immunohistochemistry on days 10-30. These findings are significant because replication of virus in the ovary could cause ovarian dysfunction, resulting in reduced fertility.
Thermal decompositions of solid amino acids in relation to their hydrogen bonds. I. Kinetic studies on the thermal decomposition of solid cystine. (1985)

The solid phase thermal decompositions of L-cystine and its three stereoisomers have been investigated in vacuo between 150 and 230°C. The decomposition processes have been examined by measuring the total pressure and the partial pressures of the four gaseous products, NH3, H2O, H2S, and CO2, as well as by the semiquantitative determination of sulfur polymers. The rate equation for the thermal decomposition of L-cystine can be approximated as zeroth order, with an induction period at the initial stage of the decomposition. A remarkable change in the reaction rate was found at around 170-180°C, above which evaporated sulfur polymers can be detected. At lower temperature the dehydration reaction is predominant, while the rates of formation of NH3, H2S, and CO2 become much larger than that of H2O as the temperature increases. The observed induction periods at T<200°C are different for each of the product gases, and depend strongly on the decomposition temperature and the history of the starting materials. The reactions that occur during this period are discussed. The different behavior observed in the thermal reactions of other sulfur-containing amino acids, L-cysteine and L-methionine, and some non sulfur-containing ones are discussed in relation to the different strengths of the hydrogen bond networks in the crystalline states.
A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici (2017)

Spore pigmentation is very common in the fungal kingdom. The best studied pigment in fungi is melanin which coats the surface of single cell spores. What and how pigments function in a fungal species with multiple cell conidia is poorly understood. Here, we identified and deleted a polyketide synthase (PKS) gene PfmaE and showed that it is essential for multicellular conidial pigmentation and development in a plant endophytic fungus, Pestalotiopsis fici. To further characterize the melanin pathway, we utilized an advanced Aspergillus nidulans heterologous system for the expression of the PKS PfmaE and the Pfma gene cluster. By structural elucidation of the pathway metabolite scytalone in A. nidulans, we provided chemical evidence that the Pfma cluster synthesizes DHN melanin. Combining genetic deletion and combinatorial gene expression of Pfma cluster genes, we determined that the putative reductase PfmaG and the PKS are sufficient for the synthesis of scytalone. Feeding scytalone back to the P. fici ΔPfmaE mutant restored pigmentation and multicellular adherence of the conidia. These results cement a growing understanding that pigments are essential not simply for protection of spores from biotic and abiotic stresses but also for spore structural development.
Comparison of blocking and blurring metrics for video compression (2006)

We evaluate the performance on compressed video of a number of available similarity, blocking, and blurring quality metrics. Using a systematic, objective framework based on simple subjective comparisons, we evaluate the ability of each metric to rank images correctly according to the subjective impact of differences in spatial content, quantization parameters, amounts of filtering, distances from the most recent I-frame, and long-term frame prediction strategies. The indicated weaknesses of available metrics can be used as guides in the development of future quality metrics.
Semantic Applications Enabling Reasoning in Product Assembly Ontologies—Moving Past Modeling (2011)

In this paper, the authors postulate an approach to introduce reasoning capabilities into ontologies in the product assembly domain in order to truly exploit these logic-based and formal representations for product data. A model containing semantic applications with multiple reasoning units in logic reasoning layer of a layered semantic application architecture is proposed. Retrieval specifications and inference rules in SWRL/SQWRL are defined in these reasoning units. Besides, local-based user interfaces have been developed to allow product engineers to submit reasoning tasks and view querying retrievals or inference results. The approach and semantic applications are illustrated with two case studies in the product assembly domain. It is demonstrated that this approach not only enables existing product data to be queried and retrieved but also enables new product data, which is not explicitly expressed in the ontology models, to be derived. It is concluded that the reasoning mechanism exploits and extends the semantic representation made possible through the ontology and thus holds promise for improved knowledge discovery and understanding.
Prey-Capture Strategies of Fish-Hunting Cone Snails: Behavior, Neurobiology and Evolution (2015)

The venomous fish-hunting cone snails (Conus) comprise eight distinct lineages evolved from ancestors that preyed on worms. In this article, we attempt to reconstruct events resulting in this shift in food resource by closely examining patterns of behavior, biochemical agents (toxins) that facilitate prey capture and the combinations of toxins present in extant species. The first sections introduce three different hunting behaviors associated with piscivory: 'taser-and-tether', 'net-engulfment' and 'strike-and-stalk'. The first two fish-hunting behaviors are clearly associated with distinct groups of venom components, called cabals, which act in concert to modify the behavior of prey in a specific manner. Derived fish-hunting behavior clearly also correlates with physical features of the radular tooth, the device that injects these biochemical components. Mapping behavior, biochemical components and radular tooth features onto phylogenetic trees shows that fish-hunting behavior emerged at least twice during evolution. The system presented here may be one of the best examples where diversity in structure, physiology and molecular features were initially driven by particular pathways selected through behavior.