gebhart/patrepeval huggingface dataset:
Evolution and function of Tmc genes in mammalian hearing (2020)

Auditory sensation in the mammalian inner ear requires mechanosensitive hair cells and an elaborate array of molecules that form the sensory transduction machinery. Several components of this machine have been identified, yet how the ensemble functions in harmony to enable the sense of hearing has not been clarified. We review recent evidence supporting the role of key transduction molecules and focus on TMC1 and TMC2, pore-forming proteins at the heart the mechanosensory device. We consider how vertebrate TMCs changed during evolution and how they function in concert with other components of the transduction apparatus. We also examine the role of TMCs in non-mammalian systems to gain insight into common themes for TMC function and properties unique to mammalian hair cell TMCs. Although the tempo of discovery has accelerated, important questions remain which will need to be addressed for a comprehensive understanding of mechanosensory transduction in the mammalian inner ear.
Consolidation therapy for ovarian cancer (2005)

Purpose. To review all the published randomized trials of consolidation therapy in ovarian cancer, including chemotherapy, radiotherapy, and potential targeted/biologic agents.Design. A Medline search was conducted to identify all publications on consolidation therapy in ovarian cancer. Proceedings of national and international meetings were also searched.Results. Platinum-based consolidation therapy is difficult to tolerate and does not confer a survival benefit. Prolonged Paclitaxel therapy lengthens the recurrence-free interval, with increased neurotoxicity. Intraperitoneal (IP) consolidation therapy is limited by marginal clinical acceptance and catheter-related complications. Oral consolidation regimens have not yet been evaluated in a randomized study. IP 32P is ineffective. Whole-abdominal radiotherapy (WAR) improves the progression-free but not overall survival in selected patients. Late radiation toxicities remain a concern with WAR. Oregovamab, an antibody to CA-125, is presently under evaluation. To date, the impact of consolidation therapy on quality-of-life remains unclear.Conclusion. An effective, minimally toxic agent for consolidation therapy in ovarian cancer has not yet been identified.
Unequal Impact of COL1A1 and COL1A2 Variants on Dentinogenesis Imperfecta (2023)

Dentinogenesis imperfecta (DI) is the main orodental manifestation of osteogenesis imperfecta (OI) caused by <i>COL1A1</i> or <i>COL1A2</i> heterozygous pathogenic variants. Its prevalence varies according to the studied population. Here, we report the molecular analysis of 81 patients with OI followed at reference centers in Brazil and France presenting <i>COL1A1</i> or <i>COL1A2</i> variants. Patients were submitted to clinical and radiographic dental examinations to diagnose the presence of DI. In addition, a systematic literature search and a descriptive statistical analysis were performed to investigate OI/DI phenotype-genotype correlation in a worldwide sample. In our cohort, 50 patients had <i>COL1A1</i> pathogenic variants, and 31 patients had <i>COL1A2</i> variants. A total of 25 novel variants were identified. Overall, data from a total of 906 individuals with OI were assessed. Results show that DI was more frequent in severe and moderate OI cases. DI prevalence was also more often associated with <i>COL1A2</i> (67.6%) than with <i>COL1A1</i> variants (45.4%) because <i>COL1A2</i> variants mainly lead to qualitative defects that predispose to DI more than quantitative defects. For the first time, 4 DI hotspots were identified. In addition, we showed that 1) glycine substitution by branched and charged amino acids in the α2(I) chain and 2) substitutions occurring in major ligand binding regions-MLRB2 in α1(I) and MLBR 3 in α2(I)-could significantly predict DI (<i>P</i> < 0.05). The accumulated variant data analysis in this study provides a further basis for increasing our comprehension to better predict the occurrence and severity of DI and appropriate OI patient management.
Carbocupration of cyclopropene. Asymmetric synthesis of quaternary carbon centers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbocupration of cyclopropene. Asymmetric synthesis of quaternary carbon centersMasahiko Isaka and Eiichi NakamuraCite this: J. Am. Chem. Soc. 1990, 112, 20, 7428–7430Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00176a072https://doi.org/10.1021/ja00176a072research-articleACS PublicationsRequest reuse permissionsArticle Views544Altmetric-Citations71LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Passive immunity to control Bovine coronavirus diarrhea in a dairy herd in Argentina (2017)

Bovine coronavirus (BCoV) is a viral enteric pathogen associated with calf diarrhea worldwide being, in Argentina, mostly detected in dairy husbandry systems. The aim of the present work was to study if maternal IgG1 antibodies (Abs) to BCoV acquired by colostrum intake modulate the development of BCoV infection in calves reared in a dairy farm in Argentina. Thirty Holstein calves were monitored during their first 60 days of age. Animals were classified into two groups depending on their initial BCoV IgG1 Ab titers. The "failure of passive transfer" (FPT) group had significantly lower IgG1 Abs to BCoV than the "acceptable passive transfer" (APT) group of calves (log10 1.98 vs. 3.38 respectively) (p<0.0001). These differences were also observed when the total protein levels in both groups were compared (p=0.0081). Moreover, 71% (5/7) of calves from the FPT group showed IgG1 seroconversion to BCoV compared to 29.4% (5/17) of animals from the APT group. Regarding viral circulation, BCoV was detected in 10% (3/30) of all calves and BCoV IgG1 Ab seroconversion was detected in 42% of the total animals showing that almost half of the calves were infected with BCoV. In conclusion, calves with high titers of specific BCoV IgG1 (≥1024) were mostly protected against viral infection, while animals with low titers of IgG1 (<1024) were mostly infected with BCoV. IgG1 Abs from colostrum origin are critical for prevention of BCoV infection.
Synthesis and insecticidal activity of 3‐aminoquinazolinone derivatives (1999)

The discovery, structure–activity relationships and insecticidal properties of R-768 (1-propionyl-3- (3-pyridylmethylamino)- 1,2,3,4- tetrahydroquinazolin- 2-one) and related compounds are described. © 1999 Society of Chemical Industry
A NEW TURBIDITY METER FOR MONITORING THE QUALITY OF WATER (1998)

The clarity of the water which is affected by the concentration of suspended particles is a measure of its quality. In this paper the design and fabrication of a turbidity meter is presented. Its operation is based on the principle that the intensity of the light scattered by the suspended matter is proportional to its concentration. Unlike the commercially available turbidity meters, which are relatively expensive and bulky, the proposed device is small-sized, lightweight, easy to use, reliable and inexpensive. This is achieved by employing a fiber link and a laser diode source. Moreover, its small size allows in situ measurements with satisfactory spatial resolution. It should be noted that the colour of the water does not affect the measurements with the new probe, which has a very good response to the changes of water turbidity. Laboratory tests of the device have yielded satisfactory repeatability and stability.
Model reactions for the metabolism of thyroxine. I. Nonenzymic cleavage of the diphenyl ether linkage of 3'-hydroxythyropropionic acid (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModel reactions for the metabolism of thyroxine. I. Nonenzymic cleavage of the diphenyl ether linkage of 3'-hydroxythyropropionic acidTeruo Matsuura, Tomoaki Nagamachi, Akira Nishinaga, Hideo Kon, and H. J. CahnmannCite this: J. Org. Chem. 1969, 34, 9, 2554–2558Publication Date (Print):September 1, 1969Publication History Published online1 May 2002Published inissue 1 September 1969https://pubs.acs.org/doi/10.1021/jo01261a015https://doi.org/10.1021/jo01261a015research-articleACS PublicationsRequest reuse permissionsArticle Views56Altmetric-Citations6LEARN 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
Los santuarios cavernosos. Un estudio del uso ceremonial de abrigos rocosos en los páramos de Mérida (1996)

By combining ethnohistorical, ethnographic and archaeological sources, it is possible to draw some conclusions about the indigenous origin and importance over time of beliefs and symbolic manifestations connected with the use of rock shelters in the paramo of Merida, for ceremonial or everyday purposes.
DynaMine (2005)

A great deal of attention has lately been given to addressing software bugs such as errors in operating system drivers or security bugs. However, there are many other lesser known errors specific to individual applications or APIs and these violations of application-specific coding rules are responsible for a multitude of errors. In this paper we propose DynaMine, a tool that analyzes source code check-ins to find highly correlated method calls as well as common bug fixes in order to automatically discover application-specific coding patterns. Potential patterns discovered through mining are passed to a dynamic analysis tool for validation; finally, the results of dynamic analysis are presented to the user.The combination of revision history mining and dynamic analysis techniques leveraged in DynaMine proves effective for both discovering new application-specific patterns and for finding errors when applied to very large applications with many man-years of development and debugging effort behind them. We have analyzed Eclipse and jEdit, two widely-used, mature, highly extensible applications consisting of more than 3,600,000 lines of code combined. By mining revision histories, we have discovered 56 previously unknown, highly application-specific patterns. Out of these, 21 were dynamically confirmed as very likely valid patterns and a total of 263 pattern violations were found.
GENETIC AND BIOCHEMICAL STUDIES OF THE AGOUTI–ATTRACTIN SYSTEM (2002)

Pleiotropic effects of melanocortin signaling were first described nearly 100 years ago when mice carrying the lethal yellow (A(y)) allele of the Agouti coat color gene were recognized to develop increased growth and adiposity. Work from our laboratory and others over the last several years has demonstrated that the non-pigmentary effects of A(y) are caused by ectopic expression of Agouti protein, a paracrine signaling molecule whose normal function is to inhibit signaling through the melanocortin 1 receptor (Mc1r), but which can mimic the effects of Agouti-related protein (Agrp), a homologous neuropeptide produced in the medial portion of the arcuate nucleus that acts as a potent antagonist of the Mc3r and Mc4r. Recently we have used the genetics of pigmentation as an in vivo screening system to analyze other mutations in the Agouti-melanocortin pathway, leading to the identification of Attractin (Atrn), a widely expressed type I transmembrane protein that serves as an accessory receptor for Agouti protein. Surprisingly, homologs of Atrn are found in fruitflies and nematodes, even though Agouti and/or Agouti-related protein are found only in vertebrates. Insight into this apparent paradox now comes from studies of different Atrn alleles, in which we find hyperactivity, abnormal myelination, and widespread CNS vacuolation. We suggest that the neurodegenerative phenotype reflects the ancestral function of Atrn to facilitate and/or maintain cell-cell interactions in the nervous system. Expression in neurectodermal cells during vertebrate evolution may have allowed Atrn to be recruited by the Agouti-melanocortin system to control coat color.
Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies (2012)

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.
Automatic Kellgren-Lawrence grade estimation driven deep learning algorithms (2020)

Knee osteoarthritis (OA) is a prevalent and disabling degenerative joint disease. Objectively identifying knee OA severity is challenging given significant inter-reader variability due to human interpretation factors. The Kellgren-Lawrence (KL) grading system is a commonly used scale to quantitatively characterize the severity of knee OA in knee radiographs. It is important to reliably identify severe knee OA since total knee arthroplasty (TKA) can provide significant improvement in patient quality of life for patients with severe knee OA. In this study, we demonstrate a deep learning approach to automatically assessing KL grades. Our approach uses faster R-CNN object detection network to identify the knee region and deep convolutional neural network for classification. We used a dataset of 7962 knee radiographs for each posteroanterior (PA) and lateral (LAT) views, to develop and evaluate our approach. Images with their corresponding KL grades were obtained from the Multicenter Osteoarthritis Study (MOST) dataset. Our network showed multi-class classification accuracy of 69.15 % when the assessment was made based on PA views and accuracy of 56.68 % when LAT views were used. The developed network may play a significant role in surgical decision-making regarding knee replacement surgery.
SARS-CoV-2 and COVID-19: The most important research questions (2020)

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Here we highlight nine most important research questions concerning virus transmission, asymptomatic and presymptomatic virus shedding, diagnosis, treatment, vaccine development, origin of virus and viral pathogenesis.
Calcium as a versatile second messenger in the control of gene expression (1999)

The elevation of intracellular calcium is a major effector of stimulus-induced physiological change in a variety of cell types. Such change is invariably complex and frequently involves the activation of gene expression. Calcium signals are often able to activate different subsets of genes within the same cell, the basis for which has been unclear. Recent studies have revealed that a number of differing properties of the calcium signal are responsible for distinct cellular responses. Microsc. Res. Tech. 46:348–355, 1999. © 1999 Wiley-Liss, Inc.
Formation of hexagonal columnar phases by heterocyclic pyrimidine derivatives (2002)

Abstract The synthesis, characterization, and mesomorphic properties of a new type of heteronuclear compounds derived from pyrimidine as core group are reported. These compounds were prepared by condensation reactions of appropriate acetophenones and benzonitriles in the presence of trifluoromethanesulphonic anhydride. They were characterized by 1H and 13C NMR spectroscopy and elemental analysis, and their phase transitions characterized and studied by thermal analysis and polarizating microscopy. These compounds exhibit hexagonal columnar (Colh) phases, as expected for disk-like molecules; the formation of columnar phases was found to be dependent on the numbers of alkoxy side chains attached. For those compounds having the same numbers of flexible side chains attached, the one with a preferred unsymmetric structure exhibited better mesomorphic properties. The observed improved mesomorphic behaviour of these compounds over other similar all-carbon heterocyclic compounds is attributed to the greater polarization of nitrogen atoms in the core ring.
SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis (2020)

The effect of the rapid accumulation of nonsynonymous mutations on the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not yet known. The 3a protein is unique to SARS-CoV and is essential for disease pathogenesis. Our study aimed at determining the nonsynonymous mutations in the 3a protein in SARS-CoV-2 and determining and characterizing the protein's structure and spatial orientation in comparison to those of 3a in SARS-CoV. A total of 51 different nonsynonymous amino acid substitutions were detected in the 3a proteins among 2,782 SARS-CoV-2 strains. We observed microclonality within the ORF3a gene tree defined by nonsynonymous mutations separating the isolates into distinct subpopulations. We detected and identified six functional domains (I to VI) in the SARS-CoV-2 3a protein. The functional domains were linked to virulence, infectivity, ion channel formation, and virus release. Our study showed the importance of conserved functional domains across the species barrier and revealed the possible role of the 3a protein in the viral life cycle. Observations reported in this study merit experimental confirmation.<b>IMPORTANCE</b> At the surge of the coronavirus disease 2019 (COVID-19) pandemic, we detected and identified six functional domains (I to VI) in the SARS-CoV-2 3a protein. Our analysis showed that the functional domains were linked to virulence, infectivity, ion channel formation, and virus release in SARS-CoV-2 3a. Our study also revealed the functional importance of conserved domains across the species barrier. Observations reported in this study merit experimental confirmation.
Camera calibration and the search for infinity (1999)

This paper considers the problem of self-calibration of a camera from an image sequence in the case where the camera's internal parameters (most notably focal length) may change. The problem of camera self-calibration from a sequence of images has proven to be a difficult one in practice, due to the need ultimately to resort to non-linear methods, which have often proven to be unreliable. In a stratified approach to self-calibration, a projective reconstruction is obtained first and this is successively refined first to an affine and then to a Euclidean (or metric) reconstruction. It has been observed that the difficult step is to obtain the affine reconstruction, or equivalently to locate the plane at infinity in the projective coordinate frame. The problem is inherently non-linear and requires iterative methods that risk not finding the optimal solution. The present paper overcomes this difficulty by imposing chirality constraints to limit the search for the plane at infinity to a 3-dimensional cubic region of parameter space. It is then possible to carry out a dense search over this cube in reasonable time. For each hypothesised placement of the plane at infinity, the calibration problem is reduced to one of calibration of a nontranslating camera, for which fast non-iterative algorithms exist. A cost function based on the result of the trial calibration is used to determine the best placement of the plane at infinity. Because of the simplicity of each trial, speeds of over 10,000 trials per second are achieved on a 256 MHz processor. It is shown that this dense search allows one to avoid areas of local minima effectively and find global minima of the cost function.
On “Successful Management of Foot Drop by Nerve Transfers to the Deep Peroneal Nerve” (J Reconstr Microsurg 2008;24:419–428) (2010)

We read with great interest the original paper by Nath et al entitled “Successful Management of Foot Drop by Nerve Transfers to the Deep Peroneal Nerve.” The authors describe the transfer of nerve fascicles of either the superficial peroneal nerve or the tibial nerve to reinnervate deep peroneal nerve innervated muscle groups in patients with peroneal nerve injuries.