gebhart/patrepeval huggingface dataset:
Pathogenicity and Diagnosis of H5N2 Mexican Avian Influenza Viruses in Chickens (1997)

Chickens were inoculated with one of five H5N2 Mexican-origin avian influenza virus (AIV) isolates to determine their pathogenicity for chickens and to determine the ability of routine virologic and serologic tests to detect infections. In laboratory infections, three AIVs, H5/94, M5/94, and J12/94, produced sporadic illness and death and were categorized as mildly pathogenic. Q1/95 produced illness and death in all inoculated chickens and was categorized as highly lethal and highly pathogenic (HP). P11/94B commonly produced clinical illness, but deaths were infrequent. During the presence of clinical signs, oropharyngeal swabs were superior for isolation of AIV, but cloacal swabs were more successful after disappearance of clinical signs. Agar gel precipitin (AGP) serologic test was superior for detecting AIV infection during the clinical phase, but AGP and hemagglutinin inhibition tests were equally effective in detecting infections after recovery from clinical illness. Passage of P11/94B parent stock and selected 14-day-embryo-passed AIVs in adult hens resulted in emergence of some HP AIV derivatives. The hemagglutinin of Q1/95 and P11/ 94B parent stock and derivative AIVs had an identical proteolytic cleavage site of.... Pro-Gln-Arg-Lys-Arg-Lys-Thr-Arg-Gly, consistent with AIVs of high pathogenicity. However, no consistent differences were identified in the sequence of the hemagglutinin gene to explain the discrepancy in lethality patterns of the P11/94B AIVs. This suggests that genes other than the hemagglutinin impact the full expression of high lethality of Mexican-origin AIV infections in chickens.
Trichodiene Synthase. Substrate Specificity and Inhibition (1995)

The substrate specificity of the sesquiterpene synthase trichodiene synthase was examined by determining the Vmax and Km parameters for the natural substrate, trans,trans-farnesyl diphosphate (1), its stereoisomer, cis,trans-farnesyl diphosphate, and the tertiary allylic isomer, (3R)-nerolidyl diphosphate (3), using both the native fungal and recombinant enzymes. A series of farnesyl diphosphate analogs, 15, 16, 20, 7, 8, and 9, was also tested as inhibitors of trichodiene synthase. 10-Fluorofarnesyl diphosphate (15) was the most effective competitive inhibitor, with a K1 of 16 nM compared to the Km for 1 of 87 nM, while the ether analog of farnesyl diphosphate, 8, an extremely potent inhibitor of squalene synthase, showed only modest inhibition of trichodiene synthase, with a K1/Km of 70.
Conics - a Poor Man's Elliptic Curves (2003)

The aim of this article is to show that the arithmetic of Pell conics admits a description which is completely analogous to that of elliptic curves: there is a theory of 2-descent with associated Selmer and Tate-Shafarevich groups, and there should be an analog of the conjecture of Birch and Swinnerton-Dyer.
Classification-Reconstruction Learning for Open-Set Recognition (2019)

Open-set classification is a problem of handling `unknown' classes that are not contained in the training dataset, whereas traditional classifiers assume that only known classes appear in the test environment. Existing open-set classifiers rely on deep networks trained in a supervised manner on known classes in the training set; this causes specialization of learned representations to known classes and makes it hard to distinguish unknowns from knowns. In contrast, we train networks for joint classification and reconstruction of input data. This enhances the learned representation so as to preserve information useful for separating unknowns from knowns, as well as to discriminate classes of knowns. Our novel Classification-Reconstruction learning for Open-Set Recognition (CROSR) utilizes latent representations for reconstruction and enables robust unknown detection without harming the known-class classification accuracy. Extensive experiments reveal that the proposed method outperforms existing deep open-set classifiers in multiple standard datasets and is robust to diverse outliers.
Revisiting the protein-coding gene catalog ofDrosophila melanogasterusing 12 fly genomes (2007)

The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in the D. melanogaster genome. We have reviewed these predictions by manual curation and validated a subset by directed cDNA screening and sequencing, revealing both new genes and new alternative splice forms of known genes. We also used these evolutionary signatures to evaluate existing gene annotations, resulting in the validation of 87% of genes lacking descriptive names and identifying 414 poorly conserved genes that are likely to be spurious predictions, noncoding, or species-specific genes. Furthermore, our methods suggest a variety of refinements to hundreds of existing gene models, such as modifications to translation start codons and exon splice boundaries. Finally, we performed directed genome-wide searches for unusual protein-coding structures, discovering 149 possible examples of stop codon readthrough, 125 new candidate ORFs of polycistronic mRNAs, and several candidate translational frameshifts. These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster.
Preventive treatment of migraine (2006)

Migraine is a common episodic pain disorder, the treatment of which can be acute to stop an attack or preventive to reduce the frequency, duration or severity of attacks. Preventive treatment is used when attacks are frequent or disabling. Many different medication groups are used for preventive treatment, including β-blockers, antidepressants and antiepileptic drugs. Their mechanisms of action include raising the threshold to migraine activation, enhancing antinociception, inhibiting cortical spreading depression, inhibiting peripheral and central sensitization, blocking neurogenic inﬂammation and modulating sympathetic, parasympathetic or 5-HT tone. In this article, I review evidence of the effectiveness of migraine preventive drugs. I also discuss the setting of treatment priorities.
Traumatic brain injury: Can the consequences be stopped? (2008)

Traumatic brain injury is a leading cause of morbidity and death in both industrialized and developing countries. To date, there is no targeted pharmacological treatment that effectively limits the progression of secondary injury. The delayed progression of deterioration of grey and white matter gives hope that a meaningful intervention can be applied in a realistic timeframe following initial trauma. In this review we discuss new insights into the subcellular mechanisms of secondary injury that have highlighted numerous potential targets for intervention.
Multivariate Matching Methods That are Equal Percent Bias Reducing, II: Maximums on Bias Reduction for Fixed Sample Sizes (1976)

Matched sampling is a method of data collection designed to reduce bias and variability due to specific matching variables. Although often used to control for bias in studies in which randomization is practically impossible, there is virtually no statistical literature devoted to investigating the ability of matched sampling to control bias in the common case of many matching variables. An obvious problem in studying the multivariate matching situation is the variety of sampling plans, underlying distributions, and intuitively reasonable matching methods. This article considers one class of multivariate matching methods which yield the same percent reduction in expected bias for each of the matching variables. The primary result is the derivation of the expression for the maximum attainable percent reduction in bias given fixed distributions and fixed sample sizes. An examination of trends in this maximum leads to a procedure for estimating minimum ratios of sample sizes needed to obtain well-matched samples.
Hormonal Regulation of Tumor Necrosis Factor‐α, Interleukin‐12 and Interleukin‐10 Production by Activated Macrophages: A Disease‐modifying Mechanism in Rheumatoid Arthritis and Systemic Lupus Erythematosus? (1999)

Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) frequently develop and progress in settings in which sympathoadrenomedullary and gonadal hormone levels are changing, e.g., during pregnancy, postpartum period, menopause, estrogen administration. This paper addresses the view that adrenal and gonadal hormonal deficiency facilitates excessive macrophage production of TNF-alpha and IL-12 that characterizes RA, whereas excessive estrogen action is suggested to play an essential role in the production of IL-10 in patients with SLE. Disease activity in SLE, in contrast to RA, appears to be associated with high-level production of IL-10, relative to the proinflammatory cytokines, TNF-alpha and IL-12. Accumulating data suggest that novel therapeutic approaches may ultimately be developed from continued investigation of the role of the neuroendocrine factors in RA and SLE.
Amphotericin B-Induced Oxidative Damage and Killing of Candida albicans (1986)

Amphotericin B (AmB) is known to bind to ergosterol in fungal cell membranes, but the precise mechanism of its toxicity to cells is as yet poorly understood. AmB autooxidizes, and it is possible that its antifungal effects could result from oxidative damage. Exposure of protoplasts of Candida albicans to AmB under hypoxic conditions reduced protoplast lysis by as much as 80% compared with incubations in air. Protoplasts were protected from AmB-induced lysis by exogenous catalase and/or superoxide dismutase (SOD). Whole cells of C. albicans were protected by exogenous catalase from AmB-induced leakage of [3H]leucine and from killing by AmB. Cells grown on medium inducing high levels of endogenous catalase were resistant to AmB-induced growth inhibition. In contrast, AmB-induced K+ leakage was not hindered under hypoxic conditions or in the presence of catalase or SOD. Thus the lethal and lytic effects of AmB on C. albicans cells and protoplasts, but not prelethal AmB-induced K+ leakage, are mediated by oxidative damage.
Paving the Path toward Porcine Organs for Transplantation (2017)

The pig heart is a candidate organ for xenotransplantation, but endogenous retroviruses (ERVs) in the pig genome can infect human cells in vitro, raising the specter of zoonotic infection. A recent report describes the generation of healthy pigs free of replication-competent ERVs.
The application of a lentiviral vector for gene transfer in fetal human hepatocytes (2000)

These studies establish that human hepatocytes are amenable to lentiviral gene transfer with sustained transgene expression. Incorporation of lentiviral vectors will be helpful in testing strategies for hepatic gene therapy.
Neonatal Respiratory Syncytial Virus Infection (1979)

Respiratory syncytial virus infections are thought to be uncommon in the first month of life. During a community outbreak, we prospectively studied such infection in our neonatal units. Of 82 neonates studied, 66 were hospitalized for six days or longer, and 23 (35 per cent) acquired this virus. Four infants died, two unexpectedly. Infected infants had a significantly shorter gestation and birth weight. Illness was often atypical, with nonspecific signs, especially in infants under three weeks of age, who had significantly less lower-respiratory-tract involvement and lower quantities of virus in their nasal washes. The titer of virus shed correlated with the infants' postnatal, but not gestational, age. Infection was also acquired by 34 per cent of the staff, who appeared to be important in the spread of the virus. These findings suggest that respiratory syncytial virus may readily infect neonates, but the disease may be atypical and may be overlooked.
Serial Killing of Tumor Cells by Human Natural Killer Cells – Enhancement by Therapeutic Antibodies (2007)

Our data suggest that NK cell-based therapies for overcoming tumors rely on their serial killing ability. Therefore, strategies augmenting the killing ability of NK cells can boost the immune system and enhance the effectiveness of monoclonal antibody-based therapies.
Differential regulation of Hsp70 subfamilies by the eukaryotic DnaJ homologue YDJ1 (1994)

In Saccharomyces cerevisiae Ydj1p, a DnaJ homolog, is localized to the cytosol with the Ssa and Ssb Hsp70 proteins. Ydj1p helps facilitate polypeptide translocation across mitochondrial and endoplasmic reticulum membranes (Caplan, A. J., Cyr, D. M., and Douglas, M. G. (1992) Cell 71, 1143-1155) and can directly interact with Ssa1p to regulate chaperone activity (Cyr, D. M., Lu, X., and Douglas, M. G. (1992) J. Biol. Chem. 267, 20927-20931). In this study, the role of Ydj1p in modulating ATP-dependent reactions catalyzed by Ssa and Ssb Hsp70 proteins has been examined using purified components and compared with that of other Hsp70 homologs BiP and DnaK. Ssa1p, Ssa2p, and Ssb1/2p all formed stable complexes with the mitochondrial presequence peptide, F1 beta(1-51). ATP alone had only modest effects on polypeptide complex formation with Ssa1p and Ssa2p, but prevented the majority of polypeptide binding to BiP and DnaK. ATP by itself also reduced polypeptide binding to Ssb1/2p to a level that was intermediate between that observed for the Ssa Hsp70 proteins tested and BiP and DnaK. ATP hydrolysis by Ssa1p, Ssa2p, and Ssb1/2p occurred at similar rates. Ydj1p was a potent modulator of the both the ATPase and polypeptide binding activities of Ssa1p and Ssa2p. In contrast, Ydj1p had little effect on the ATPase and polypeptide binding activity of Ssb1/2p. Therefore the chaperone-related activities of Ssa and Ssb Hsp70 proteins exhibit significant differences in sensitivity to ATP and YDJ1p. These data indicate that regulation of Hsp70 activity by DnaJ homologs can be specific. The specificity of interactions between Ydj1p and the Ssa and Ssb Hsp70 proteins observed could contribute in determining the functional specificity of these chaperones in the cytosol. In related experiments, F1 beta(1-51) was found to reduce the extent to which Ydj1p stimulated Ssa1p ATPase activity. This effect correlated with the formation of F1 beta(1-51).Ssa1p complexes. We propose that intramolecular communication between the polypeptide binding, ATPase and DnaJ regulatory domains on Ssa1p plays a role in the regulation of chaperone activity.
Disruption of prion rods generates 10-nm spherical particles having high alpha-helical content and lacking scrapie infectivity (1996)

An abnormal isoform of the prion protein (PrP) designated PrPSc is the major, or possibly the only, component of infectious prions. Structural studies of PrPSc have been impeded by its lack of solubility under conditions in which infectivity is retained. Among the many detergents examined, only treatment with the ionic detergent sodium dodecyl sulfate (SDS) or Sarkosyl followed by sonication dispersed prion rods which are composed of PrP 27-30, an N-terminally truncated form of PrPSc. After ultracentrifugation at 100,000 x g for 1 h, approximately 30% of the PrP 27-30 and scrapie infectivity were found in the supernatant, which was fractionated by sedimentation through 5 to 20% sucrose gradients. Near the top of the gradient, spherical particles with an observed sedimentation coefficient of approximately 6S, approximately 10 mm in diameter and composed of four to six PrP 27-30 molecules, were found. The spheres could be digested with proteinase K and exhibited little, if any, scrapie infectivity. When the prion rods were disrupted in SDS and the entire sample was fractionated by sucrose gradient centrifugation, a lipid-rich fraction at the meniscus composed of fragments of rods and heterogeneous particles containing high levels of prion infectivity was found. Fractions adjacent to the meniscus also contained spherical particles. Circular dichroism of the spheres revealed 60% alpha-helical content; addition of 25% acetonitrile induced aggregates high in beta sheet but remaining devoid of infectivity. Although the highly purified spherical oligomers of PrP 27-30 lack infectivity, they may provide an excellent substrate for determining conditions of renaturation under which prion particles regain infectivity.
Emx2regulates the proliferation of stem cells of the adult mammalian central nervous system (2002)

The appropriate control of proliferation of neural precursors has fundamental implications for the development of the central nervous system and for cell homeostasis/replacement within specific brain regions throughout adulthood. The role of genetic determinants in this process is largely unknown. We report the expression of the homeobox transcription factor Emx2 within the periventricular region of the adult telencephalon. This neurogenetic area displays a large number of multipotent stem cells. Adult neural stem cells isolated from this region do express Emx2 and down-regulate it significantly upon differentiation into neurons and glia. Abolishing or, increasing Emx2 expression in adult neural stem cells greatly enhances or reduces their rate of proliferation, respectively. We determined that altering the expression of Emx2 affects neither the cell cycle length of adult neural stem cells nor their ability to generate neurons and glia. Rather, when Emx2 expression is abolished, the frequency of symmetric divisions that generate two stem cells increases, whereas it decreases when Emx2 expression is enhanced.
Image de-fencing (2008)

We introduce a novel image segmentation algorithm that uses translational symmetry as the primary foreground/background separation cue. We investigate the process of identifying and analyzing image regions that present approximate translational symmetry for the purpose of image forground/background separation. In conjunction with texture-based inpainting, understanding the different see-through layers allows us to perform powerful image manipulations such as recovering a mesh-occluded background (as much as 53% occluded area) to achieve the effect of image and photo de-fencing. Our algorithm consists of three distinct phases- (1) automatically finding the skeleton structure of a potential frontal layer (fence) in the form of a deformed lattice, (2) separating foreground/background layers using appearance regularity, and (3) occluded foreground inpainting to reveal a complete, non-occluded image. Each of these three tasks presents its own special computational challenges that are not encountered in previous, general image de-layering or texture inpainting applications.
Distributed snapshots (1985)

This paper presents an algorithm by which a process in a distributed system determines a global state of the system during a computation. Many problems in distributed systems can be cast in terms of the problem of detecting global states. For instance, the global state detection algorithm helps to solve an important class of problems: stable property detection. A stable property is one that persists: once a stable property becomes true it remains true thereafter. Examples of stable properties are “computation has terminated,” “ the system is deadlocked” and “all tokens in a token ring have disappeared.” The stable property detection problem is that of devising algorithms to detect a given stable property. Global state detection can also be used for checkpointing.
Low-power optical bistability in a free-standing silicon ring resonator (2010)

We demonstrate low-power thermo-optic-based optical bistability in a free-standing silicon ring resonator. A bistable optical response is achieved at reduced pump powers by thermally isolating the ring resonator from its supporting substrate with an air gap. The conversion efficiency from optical power to temperature change in the silicon core is enhanced. The optical transfer function of the resulting free-standing resonator exhibits a hysteresis loop for 80 microW input optical power. Similar nonthermally isolated resonators at the same detuning do not exhibit a bistable mode for input powers less than 2 mW.
Multiple, Distinct Forms of Bovine and Human Protein Kinase C Suggest Diversity in Cellular Signaling Pathways (1986)

A new family of protein kinase C-related genes has been identified in bovine, human, and rat genomes. The alpha-, beta-, and gamma-type protein kinase sequences are highly homologous, include a kinase domain, and potential calcium-binding sites, and they contain interspersed variable regions. The corresponding genes are located on distinct human chromosomes; the possibility of even greater genetic complexity of this gene family is suggested by Northern and Southern hybridization analyses.
A CBIR method based on color-spatial feature (2003)

Along with the analysis of color features in the hue, saturation and value (HSV) space, a new dividing method to quantize the color space into 36 non-uniform bins is introduced in this paper. Based on this quantization method we propose a color-spatial method to include several spatial features of the colors in an image for retrieval. These features are area and position, which mean the zero-order and the first-order moments, respectively. Experiments on an image database of 838 images show that the algorithm performs well in precision and adaptability.
Hydrophobic‐Interaction Chromatography (1995)

This unit discusses the important parameters in designing and optimizing a separation by hydrophobic interaction chromatography (HIC), including preparing the sample and choosing a matrix, column, and buffer. Protocols are provided for packing and testing a column; determining binding and elution conditions; eluting the sample; and cleaning, regenerating, and storing HIC columns.
Dynamic textures (2002)

Dynamic textures are sequences of images of moving scenes that exhibit certain stationarity properties in time; these include sea-waves, smoke, foliage, whirlwind but also talking faces, traffic scenes etc. We present a novel characterization of dynamic textures that poses the problems of modelling, learning, recognizing and synthesizing dynamic textures on a firm analytical footing. We borrow tools from system identification to capture the "essence" of dynamic textures; we do so by learning (i.e. identifying) models that are optimal in the sense of maximum likelihood or minimum prediction error variance. For the special case of second-order stationary processes we identify the model in closed form. Once learned, a model has predictive power and can be used for extrapolating synthetic sequences to infinite length with negligible computational cost. We present experimental evidence that, within our framework, even low dimensional models can capture very complex visual phenomena.