gebhart/patrepeval huggingface dataset:
A Mouse Model of Retinal Ischemia-Reperfusion Injury Through Elevation of Intraocular Pressure (2016)

Retinal ischemia-reperfusion (I/R) is a pathophysiological process contributing to cellular damage in multiple ocular conditions, including glaucoma, diabetic retinopathy, and retinal vascular occlusions. Rodent models of I/R injury are providing significant insights into mechanisms and treatment strategies for human I/R injury, especially with regard to neurodegenerative damage in the retinal neurovascular unit. Presented here is a protocol for inducing retinal I/R injury in mice through elevation of intraocular pressure (IOP). In this protocol, the ocular anterior chamber is cannulated with a needle, through which flows the drip of an elevated saline reservoir. Using this drip to raise IOP above systolic arterial blood pressure, a practitioner temporarily halts inner retinal blood flow (ischemia). When circulation is reinstated (reperfusion) by removal of the cannula, severe cellular damage ensues, resulting ultimately in retinal neurodegeneration. Recent studies demonstrate inflammation, vascular permeability, and capillary degeneration as additional elements of this model. Compared to alternative retinal I/R methodologies, such as retinal arterial ligation, retinal I/R injury by elevated IOP offers advantages in its anatomical specificity, experimental tractability, and technical accessibility, presenting itself as a valuable tool for examining neuronal pathogenesis and therapy in the retinal neurovascular unit.
LIP: Local Importance-based Pooling (2019)

Spatial downsampling layers are favored in convolutional neural networks (CNNs) to downscale feature maps for larger receptive fields and less memory consumption. However, for discriminative tasks, there is a possibility that these layers lose the discriminative details due to improper pooling strategies, which could hinder the learning process and eventually result in suboptimal models. In this paper, we present a unified framework over the existing downsampling layers (e.g., average pooling, max pooling, and strided convolution) from a local importance view. In this framework, we analyze the issues of these widely-used pooling layers and figure out the criteria for designing an effective downsampling layer. According to this analysis, we propose a conceptually simple, general, and effective pooling layer based on local importance modeling, termed as {\em Local Importance-based Pooling} (LIP). LIP can automatically enhance discriminative features during the downsampling procedure by learning adaptive importance weights based on inputs. Experiment results show that LIP consistently yields notable gains with different depths and different architectures on ImageNet classification. In the challenging MS COCO dataset, detectors with our LIP-ResNets as backbones obtain a consistent improvement ($\ge 1.4\%$) over the vanilla ResNets, and especially achieve the current state-of-the-art performance in detecting small objects under the single-scale testing scheme.
Regulation by Insulin of Gene Expression in Human Skeletal Muscle and Adipose Tissue (2001)

Defective regulation of gene expression may be involved in the pathogenesis of type 2 diabetes. We have characterized the concerted regulation by insulin (3-h hyperinsulinemic clamp) of the expression of 10 genes related to insulin action in skeletal muscle and in subcutaneous adipose tissue, and we have verified whether a defective regulation of some of them could be specifically encountered in tissues of type 2 diabetic patients. Basal mRNA levels (determined by reverse transcriptase-competitive polymerase chain reaction) of insulin receptor, insulin receptor substrate-1, p85alpha phosphatidylinositol 3-kinase (PI3K), p110alphaPI3K, p110betaPI3K, GLUT4, glycogen synthase, and sterol regulatory-element-binding protein-1c (SREBP-1c) were similar in muscle of control (n = 17), type 2 diabetic (n = 9), type 1 diabetic (n = 9), and nondiabetic obese (n = 9) subjects. In muscle, the expression of hexokinase II was decreased in type 2 diabetic patients (P < 0.01). In adipose tissue, SREBP-1c (P < 0.01) mRNA expression was reduced in obese (nondiabetic and type 2 diabetic) subjects and was negatively correlated with the BMI of the subjects (r = -0.63, P = 0.02). Insulin (+/-1,000 pmol/l) induced a two- to threefold increase (P < 0.05) in hexokinase II, p85alphaPI3K, and SREBP-1c mRNA levels in muscle and in adipose tissue in control subjects, in insulin-resistant nondiabetic obese patients, and in hyperglycemic type 1 diabetic subjects. Upregulation of these genes was completely blunted in type 2 diabetic patients. This study thus provides evidence for a specific defect in the regulation of a group of important genes in response to insulin in peripheral tissues of type 2 diabetic patients.
Mutagen Formation in Processed Foods (1983)

The role of cooking in the formation of mutagenic substances in food is well established. Broiling, grilling and frying of foods, especially those high in protein, can produce substances which cause mutation in bacterial and mammalian in vitro systems. A large class of foods which also undergoes heat treatment but which has been overlooked in mutagen studies is commercially processed foods. This paper describes a survey of mutagenicity in various commercially heated foods, investigates the process of mutagen formation in two canned products and discusses the implications for the food industry and regulatory agencies if the mutagens formed during processing are eventually found to be carcinogenic.
Use of fast Walsh-Hadamard transformation for optimalsymbol-by-symbol binary block-code decoding (1998)

A procedure for the optimal symbol-by-symbol binary block-code decoding is presented: it uses the spectral Walsh-Hadamard transformation. The dimension of the Walsh-Hadamard basis is equal to that of dual codes. The realisation of the described procedure, using the fast Walsh-Hadamard transformation, is seen to be the most efficient in terms of computational complexity for high-rate code decoding, in comparison with known symbol-by-symbol decoding procedures.
Formal analysis of security policy implementations in enterprise networks (2009)

The management of security, operations and services in large scale enterprise networks is becoming more difficult due to complex security policies of the organizations and also due to dynamic changes in network topologies. Typically, the global security policy of an enterprise network is implemented in a distributed fashion through appropriate sets of access control rules (ACL rules) across various interface switches (layer 3 switches) in the network. In such networks, verification of the ACL implementations with respect to the security policies is a major technical challenge to the network administrators. This is difficult to achieve manually, because of the complex policy constraints (temporal access constraints) and the presence of hidden access paths in the network which may in turn violate one or more policy rules implicitly. The inconsistent hidden access paths may be formed due to transitive relationships between implemented service access paths in the network. Moreover, the complexity of the problem is compounded due to dynamic changes in network topologies. In any point of time, the failure of the network interfaces or links may change the network topology as a result alternative routing paths can be formed for forwarding various service packets. Hence, the existing security implementation (distribution of ACL rules) may not satisfy the policies. In this paper, a fault analysis module is incorporated along
Rapid, colorimetric identification of Candida albicans (1990)

A total of 706 yeast isolates were evaluated in parallel by the Candida albicans Screen (CAS; Carr-Scarborough Microbiologicals, Inc., Stone Mountain, Ga.) test and the germ tube (GT) test in comparison with the API 20C Yeast Identification System. The CAS and GT tests correctly identified 419 of the 422 isolates of C. albicans (99.3%). Two of the false-negative reactions occurring with the CAS were with GT-negative strains of C. albicans. There were two false-positive CAS reactions involving a single strain each of C. parapsilosis and C. tropicalis. Sensitivity and specificity for both tests exceeded 99%, with positive and negative predictive values of 99 and 98%, respectively.
Endocrine Activities of Cortistatin-14 and Its Interaction with GHRH and Ghrelin in Humans (2002)

Cortistatin (CST)-14, a neuropeptide with high homology with somatostatin (SS)-14, binds all sst subtypes but, unlike SS, also ghrelin's receptor. In six normal adults, we studied the effects of CST-14 or SS-14 administration (2.0 μg/kg/h iv) on: 1) GH and insulin secretion; 2) the GH response to GHRH (1.0 μg/kg iv); and 3) the GH, prolactin (PRL), ACTH, cortisol, insulin, and glucose responses to ghrelin (1.0 μg/kg iv). CST-14 inhibited GH and insulin secretion (P < 0.01) to the same extent of SS-14. The GH response to GHRH was similarly inhibited (P < 0.01) by either CST-14 or SS-14. Ghrelin released more GH than GHRH (P < 0.01); these responses were similarly inhibited (P < 0.05) by either CST-14 or SS-14, that made ghrelin-induced GH rise similar to that after GHRH alone. Neither CST-14 nor SS-14 modified PRL, ACTH, or cortisol responses to ghrelin. The inhibitory effect of CST-14 and SS-14 on insulin was unaffected by ghrelin that, in turn, reduced insulin secretion per se (P < 0.01). Ghrelin increased glucose levels (P < 0.05); CST-14 and SS-14 did not modify this effect. Thus, CST-14 inhibits both basal and stimulated GH secretion in humans to the same extent of SS-14. The GH-releasing activity of ghrelin seems partially resistant to CST-14 as well as SS-14. CST-14 and SS-14 do not affect PRL and ACTH secretion but, like ghrelin, inhibit insulin secretion; the ghrelin-induced inhibition is not additive with that of CST-14 or SS-14, suggesting a common mechanism of action on β cell secretion.
Consistent Network Update without tagging (2014)

Designing of network update algorithms is urgent for development of SDN control software. A particular case of Network Update Problem is that of adding a set of forwarding rules into flow-tables of SDN switches (say, to install new paths in the network) or restoring seamlessly a given network configuration after some packet forwarding rules have been disabled (say, at the expiry of their time-outs). Some algorithms provide solutions to these problems but only with the help of tagging techniques. But is it possible to perform a consistent network update without tagging? We study this problem in the framework of a formal model of SDN, develop correct and safe network updating algorithms, and show that in some cases it is impossible to update consistently network configurations without resorting either to tagging or to priorities of packet forwarding rules.
Monoclonal antibodies to human lung tumor antigens demonstrated by immunofluorescence and immunoprecipitation. (1982)

Various studies have demonstrated the usefulness of monoclonal antibodies in recognizing discrete tumor antigenic determinants. The present study describes the tissue reactivity of monoclonal antibodies prepared against a squamous cell carcinoma of the lung. Antigens were purified from the tumor extract by anti-beta 2 microglobulin affinity chromatography. These beta 2-associated antigens demonstrated tumor specificity by the leukocyte adherence inhibition assay. Antibody-secreting hybridomas were generated by fusion of mouse myeloma cells with mouse spleen cells immunized with purified tumor antigens. Hybridomas were selected by a solid-phase tumor membrane-binding immunoassay. The target specificity of the secreted monoclonal antibodies was ascertained by radioimmunoprecipitation analysis and indirect immunofluorescence on various human tumor and normal tissue sections. Monoclonal antibody-secreting hybridomas 48.4.8 and 48.4.2 secreted immunoglobulin that selectively immunoprecipitated polypeptide fragments from human lung tumor membrane antigens. Hybridoma 9.2.2 secreted antibody that was strongly positive by indirect immunofluorescence on all tested lung squamous cell carcinomas. Adjacent or intervening normal lung tissue did not display significant immunofluorescence. Adenocarcinomas of the lung were negative or focally positive when focal squamous cell differentiation was present. Oat cell carcinomas were negative. The secreted antibody did not significantly stain three extrapulmonary tumors or a variety of normal tissues.
Astrovirus‐Associated epidemic gastroenteritis in japan (1982)

An outbreak of epidemic gastroenteritis associated with astrovirus, the first case reported in Japan, is described. Not only children (5-6 years of age), but also staff members of a kindergarten were affected. the virus particles detected in stools were 28-30 nm in diameter with a circular outline and had the characteristic star-like configuration which allowed identification as astrovirus. Significant immune responses to the virus were confirmed by immune electron microscopy. Out of 84 children, 43 (54.2%) were affected; the common symptoms were vomiting, abdominal pain, diarrhea, and fever. All the patients recovered completely within 48 hours. Occurrence of gastroenteritis due to contact with these patients was observed in 14 of 43 families.
<i>N</i> <sup>6</sup> -Benzyladenine: Inhibitor of Respiratory Kinases (1964)

N(4)-benzyladenine, an active phytokinin, inhibits the respiration of many explants. The chemnical also delays senescence and extends the postharvest life of many green or leafy vegetables. Evidence is presented that these phenomena may be linked to a comnpetitive inhibition of the glycolytic kinases by N(4)-benzyladenine.
Effects of a fatty acid synthase inhibitor on adipocyte differentiation of mouse 3T3-L1 cells. (2004)

C75 blocked the adipocyte differentiation, which was related with down-regulation of PPARgamma mRNA.
C-Terminal Sequence Analysis of Peptides and Proteins Using Carboxypeptidases and Mass Spectrometry after Derivatization of Lys and Cys Residues (1997)

C-Terminal sequence analysis of peptides and proteins using carboxypeptidase digestion in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is convenient for protein and peptide characterization. After a short digestion, a sequence up to 20 residues can be identified, but the total number depends on the individual sequence. Due to the accuracy limits of the MALDI time-of-flight arrangement, the assignment of several residues with close mass values, including Lys/Glx, may remain ambiguous. We have used derivatization of lysine residues by guanidination to overcome the problem of Lys identification. The reaction is rapid and specific and results in full derivatization. In the case of Cys-containing peptides, problems arise from the fact that carboxypeptidases Y and P do not cleave peptides that contain nonderivatized cystine, cysteic acid, or (carboxymethyl)cysteine. Successful identification of Cys residues within the sequence is instead achieved by conversion of Cys to 4-thialaminine by (trimethylamino)-ethylation. The two derivatizations of Lys and Cys side chains provide opportunities for proton attachment and therefore facilitate the analysis by MALDI-MS. This C-terminal sequence analysis method is also useful for large proteins after fragmentation with specific enzymes.
Efficient Recovery of Carbon Dioxide from Flue Gases of Coal-Fired Power Plants by Cyclic Fixed-Bed Operations over K<sub>2</sub>CO<sub>3</sub>-on-Carbon (1998)

An efficient chemical absorption method capable of cyclic fixed-bed operations under moist conditions for the recovery of carbon dioxide from flue gases has been proposed employing K2CO3-on-carbon. Carbon dioxide was chemically absorbed by the reaction K2CO3 + CO2 + H2O ⇄ 2KHCO3 to form potassium hydrogencarbonate. Moisture, usually contained as high as 8−17% in flue gases, badly affects the capacity of conventional adsorbents such as zeolites, but the present technology has no concern with moisture; water is rather necessary in principle as shown in the equation above. Deliquescent potassium carbonate should be supported on an appropriate porous material to adapt for fixed-bed operations. After breakthrough of carbon dioxide, the entrapped carbon dioxide was released by the decomposition of hydrogencarbonate to shift the reaction in Eq.1 in reverse on flushing with steam, which could be condensed by cooling to afford carbon dioxide in high purity. Among various preparations of alkaline-earth carbonates (X2CO3, X = Li, Na, K) on porous materials, K2CO3-on-activated carbon revealed excellent properties for the present purpose. Preparation and characterization of K2CO3-on-carbon and illustrative fixed-bed operations under flue gas conditions in laboratory columns and a bench-scale plant are described.
Construction of an Artificial Pathway for Isobutanol Biosynthesis in the Cytosol of<i>Saccharomyces cerevisiae</i> (2012)

To increase isobutanol production in Saccharomyces cerevisiae, the valine biosynthetic pathway was activated by overexpression of the relevant enzymes in the mitochondria and the cytosol. Native mitochondrial enzymes were overepxressed in the cytosol by deleting the mitochondrial transit peptides. The metabolically engineered S. cerevisiae possessing the cytosolic pathway showed increased isobutanol production (63 ± 4 mg/L).
N-Chlorotaurine, a Novel Endogenous Antimicrobial Agent (2001)

Application of N-chlorotaurine to the middle ear is well tolerated without adverse effects and may be a useful new endogenous antimicrobial agent for local treatment of otologic infections.
A Framework for Observation-Based Modelling in Model-Based Testing (2010)

One of the single most important reasons that modeling and model-based testing are not yet common practice in industry is the per-ceived difficulty of making the models up to the level of detail and quality required for their automated processing. Models unleash their full potential only through sufficient formality, and after being processed by tools. However, making sufficiently formal models is regarded by industry as laborious, expensive, and overall daunting. This article presents a solution for circumventing the manual modeling process by bootstrapping and devising the model auto-matically from observations, and using that model for test case gen-eration. It describes a combination of existing techniques and tools, some of which are readily used in industry, to provide an iterative process with which test engineers can create a formal model of a component, use it to generate test stimuli, compare the observed
Hetero‐<i>ansa</i>‐Bridged Main Group Metallocenes — a Structural and NMR Study (1994)

1,2‐Bis(dimethylamino)‐1,2‐di‐9‐fluorenyldiborane(4) (1) is doubly metallated with group 1 and 2 metals to yield metal 1,2‐bis(dimethylamino)‐1,2‐di‐9‐fluorenyldiborate(4) 2‐Li to 2‐Ba. The conformations of these compounds in solution are investigated by NMR spectroscopy, and the solid‐state structures of 2‐Li · 5 THF, 2‐K · 4 THF, 2‐K · 2 DME, and 2‐Ca · 2 THF are determined by X‐ray diffraction. All four structures can be described as main group metallocenes. The potassium derivatives form contact ion pairs, leading to polymeric chain‐like structures. In contrast, 2‐Li · 5 THF exhibits the rare combination of a contact ion pair with a solventseparated ion pair, giving the monomeric structure [Li(THF) 4 ][(fl 2 B 2 (NMe 2 ) 2 )Li · THF]. 2‐Ca · 2 THF, which is also monomeric, adapts a severely distorted geometry.
Autostereoscopic 3-D display (1990)

A novel illumination scheme by which a liquid crystal display may be converted into a truly 3-D display is proposed and demonstrated.
Cervicovaginal Secretions Contribute to Innate Resistance to Herpes Simplex Virus Infection (2005)

Defining and preserving the innate antiviral activity found in cervicovaginal secretions is critical. Cervicovaginal lavage (CVL) samples were obtained from 20 healthy women and evaluated for anti-herpes simplex virus (HSV) activity. CVL samples reduced HSV-2 yields by 23-fold (median), and the anti-HSV activity of CVL samples correlated with the concentration of human neutrophil peptides (HNP)-1-3. Both CVL samples and HNP-1-3 interacted with virus and prevented entry after binding. Substantially less protective activity was observed in CVL samples obtained from 20 human immunodeficiency virus--infected subjects, but the addition of CVL samples from healthy subjects enhanced the antiviral activity. The significance of the innate activity was further demonstrated by showing that CVL samples prevented murine genital herpes. Fourteen of 15 mice were protected from genital herpes if they were challenged with HSV-2 pretreated with CVL samples from healthy subjects. In contrast, all 15 mice challenged with untreated HSV-2 died. These findings are evidence that cervicovaginal secretions contribute to innate resistance to HSV-2 and identify defensins as contributors to this activity.
Functional neuroimaging studies of the effects of psychotherapy (2014)

It has been long established that psychological interventions can markedly alter patients' thinking patterns, beliefs, attitudes, emotional states, and behaviors. Little was known about the neural mechanisms mediating such alterations before the advent of functional neuroimaging techniques. Since the turn of the new millenium, several functional neuroimaging studies have been conducted to tackle this important issue. Some of these studies have explored the neural impact of various forms of psychotherapy in individuals with major depressive disorder. Other neuroimaging studies have investigated the effects of psychological interventions for anxiety disorders. I review these studies in the present article, and discuss the putative neural mechanisms of change in psychotherapy. The findings of these studies suggest that mental and behavioral changes occurring during psychotherapeutic interventions can lead to a normalization of functional brain activity at a global level.
Successful Implementation of a Multiple-ICU Clinical Information System in a Tertiary Care Medical Center (2000)

Although the technology of clinical information systems (CIS) is constantly improving, the implementation of such systems remains a daunting task. Computerized charting represents a major paradigm and workflow shift for nurses and other caregivers trained to document on paper, and for physicians who use charts for direct patient care. In intensive care units (ICUs) these concerns are magnified due to the complexity of charting and the criticality of patient illness. Implementing a CIS across multiple specialty ICUs is an particularly difficult challenge, due to the differences in documentation and workflow in different ICUs. The issues presented here are ones that arose with implementation of an ICU CIS across a tertiary care medical center. The solutions we devised may be useful elsewhere.
Information-rich localization microscopy through machine learning (2019)

Recent years have witnessed the development of single-molecule localization microscopy as a generic tool for sampling diverse biologically relevant information at the super-resolution level. While current approaches often rely on the target-specific alteration of the point spread function to encode the multidimensional contents of single fluorophores, the details of the point spread function in an unmodified microscope already contain rich information. Here we introduce a data-driven approach in which artificial neural networks are trained to make a direct link between an experimental point spread function image and its underlying, multidimensional parameters, and compare results with alternative approaches based on maximum likelihood estimation. To demonstrate this concept in real systems, we decipher in fixed cells both the colors and the axial positions of single molecules in regular localization microscopy data.