gebhart/patrepeval huggingface dataset:
Uncovering and characterizing splice variants associated with survival in lung cancer patients (2019)

Splice variants have been shown to play an important role in tumor initiation and progression and can serve as novel cancer biomarkers. However, the clinical importance of individual splice variants and the mechanisms by which they can perturb cellular functions are still poorly understood. To address these issues, we developed an efficient and robust computational method to: (1) identify splice variants that are associated with patient survival in a statistically significant manner; and (2) predict rewired protein-protein interactions that may result from altered patterns of expression of such variants. We applied our method to the lung adenocarcinoma dataset from TCGA and identified splice variants that are significantly associated with patient survival and can alter protein-protein interactions. Among these variants, several are implicated in DNA repair through homologous recombination. To computationally validate our findings, we characterized the mutational signatures in patients, grouped by low and high expression of a splice variant associated with patient survival and involved in DNA repair. The results of the mutational signature analysis are in agreement with the molecular mechanism suggested by our method. To the best of our knowledge, this is the first attempt to build a computational approach to systematically identify splice variants associated with patient survival that can also generate experimentally testable, mechanistic hypotheses. Code for identifying survival-significant splice variants using the Null Empirically Estimated P-value method can be found at https://github.com/thecodingdoc/neep. Code for construction of Multi-Granularity Graphs to discover potential rewired protein interactions can be found at https://github.com/scwest/SINBAD.
Affective medicine: technology with emotional intelligence. (2002)

For a long time people have kept emotions out of the deliberate tools of medicine and science; scientists, physicians, and patients have often felt and sometimes expressed emotion, but no tools could sense, measure, and respond to their affective information. A series of recent studies indicates that emotions, particularly stress, anger, and depression, are important factors with serious and significant implications for health. This paper highlights research at the MIT Media Lab aimed at giving computers the ability to comfortably sense, recognize, and respond to certain aspects of human emotion, especially affective states such as frustration, confusion, interest, stress, anger, and joy. Examples of recently developed systems are shown, including computer systems that are wearable and computers that respond to people with a kind of active listening, empathy, and sympathy. Results are reported for computer recognition of emotion, for teaching affective skills to autistics, and for having computers help users manage emotions such as frustration.
MMPP modeling of aggregated ATM traffic (2002)

The paper presents a study on the use of Markov-modulated Poisson processes (MMPPs) in modeling aggregate ATM traffic in order to evaluate the queueing performance. Performance of various techniques for matching a 2-state MMPP to a superposition of on-off sources is compared. The applicability of the 2-state MMPP and its corresponding parameter matching techniques to model an arbitrary aggregate ATM traffic in evaluating its queueing performance are examined by simulation. A refined matching technique for a 2-state MMPP model is proposed. A procedure to estimate the four parameters of a 2-state MMPP from the measured arrivals suitable for the moment-based matching technique is presented. Test cases are given to illustrate the accuracy of the proposed estimation procedure. An approximation for the survivor function is derived.
O067: Poorly processed reusable dispensers for surface disinfection tissues are a possible source of infection (2013)

Reusable surface disinfectant (SD) tissue dispensers are used in hospitals in many countries because they allow immediate access to soaked tissues for targeted surface decontamination.
Network Pharmacology of Triptolide in Cancer Cells: Implications for Transcription Factor Binding (2021)

Abstract Background: Triptolide is an active natural product, which inhibits cell proliferation, induces cell apoptosis, suppresses tumor metastasis and improves the effect of other therapeutic treatments in several cancer cell lines by affecting multiple molecules and signaling pathways, such as caspases, heat-shock proteins, DNA damage and NF-ĸB. Purpose: We investigated the effect of triptolide towards NF-ĸB and GATA1. Methods: We used cell viability assay, compare and cluster analyses of microarray-based mRNA transcriptome-wide expression data, gene promoter binding motif analysis, molecular docking, Ingenuity pathway analysis, NF-ĸB reporter cell assay, and electrophoretic mobility shift assay (EMSA) of GATA1. Results: Triptolide inhibited the growth of drug-sensitive (CCRF-CEM, U87.MG) and drug-resistant cell lines (CEM/ADR5000, U87.MGΔEGFR). Hierarchical cluster analysis showed six major clusters in dendrogram. The sensitive and resistant cell lines were statistically significant ( p = 0.65 × 10 -2 ) distributed. The binding motifs of NF-κB (Rel) and of GATA1 protein were significantly enriched in regions of 25 kb upstream promoter of all genes. IPA showed the networks, biological functions, and canonical pathways influencing the activity of triptolide towards tumor cells. Interestingly, upstream analysis for the 40 genes identified by compare analysis revealed ZFPM1 (friend of GATA protein 1) as top transcription regulator. However, we did not observe any effect of triptolide to the binding of GATA1 in vitro . We confirmed that triptolide inhibited NF-κB activity, and it strongly bound to the pharmacophores of IκB kinase β and NF-κB in silico . Conclusion: Triptolide showed promising inhibitory effect toward NF-κB, making it a potential candidate for targeting NF-κB.
Microencapsulation by Complex Coacervation: Methods, Techniques, Benefits, and Applications - A Review (2016)

Complex coacervation is old method which has been used in different industrial applications. It plays an important role to protect and to control nature of active agent of a product. In this present review we tried to discuss about Complex coacervation by introducing it and Principles of making complex Coacervation, we talk also on its application in Food industry and nutrition specially in Oils and Essentials oils encapsulation and Encapsulation of Probiotic Bacteria.
Respiratory Viral Infections in Transplant Recipients (2007)

A wide range of viruses affect the respiratory tract of transplant recipients, including adenovirus, influenza, human metapneumovirus, parainfluenza virus, respiratory syncytial virus (RSV) and rhinovirus. Prospective studies using contemporary diagnostic techniques have recently improved our understanding of the epidemiology and importance of these respiratory viruses among transplant recipients. From these studies, rhinovirus, in particular, has been shown to be one of the most common causes of infection in stem cell and lung transplant recipients. In addition to epidemiological data, recent studies have also advanced our understanding of management of influenza, adenovirus, and RSV infections among transplant recipients.
Aircraft Fuel System Lightning Protection Design and Qualification Test Procedures Development. (1994)

This document has been approved tor public release.and sale; its distribution is unlimited. friis document is available to the public through tie National Technical Information
Basic circuit compilation techniques for an ion-trap quantum machine (2017)

We study the problem of compilation of quantum algorithms into optimized physical-level circuits executable in a quantum information processing (QIP) experiment based on trapped atomic ions. We report a complete strategy: starting with an algorithm in the form of a quantum computer program, we compile it into a high-level logical circuit that goes through multiple stages of decomposition into progressively lower-level circuits until we reach the physical execution-level specification. We skip the fault-tolerance layer, as it is not within the scope of this work. The different stages are structured so as to best assist with the overall optimization while taking into account numerous optimization criteria, including minimizing the number of expensive two-qubit gates, minimizing the number of less expensive single-qubit gates, optimizing the runtime, minimizing the overall circuit error, and optimizing classical control sequences. Our approach allows a trade-off between circuit runtime and quantum error, as well as to accommodate future changes in the optimization criteria that may likely arise as a result of the anticipated improvements in the physical-level control of the experiment.
Copy Number of Pilus Gene Clusters in Haemophilus influenzae and Variation in the hifE Pilin Gene (1998)

Brazilian purpuric fever (BPF)-associated Haemophilus influenzae biogroup aegyptius strain F3031 contains two identical copies of a five gene cluster (hifA to hifE) encoding pili similar to well-characterized Hif fimbriae of H. influenzae type b. HifE, the putative pilus tip adhesin of F3031, shares only 40% amino acid sequence similarity with the same molecule from type b strains, whereas the other four proteins have 75 to 95% identity. To determine whether pilus cluster duplication and the hifE(F3031) allele were special features of BPF-associated bacteria, we analyzed a collection of H. influenzae strains by PCR with hifA- and hifE-specific oligonucleotides, by Southern hybridization with a hifC gene probe, and by nucleotide sequencing. The presence of two pilus clusters was limited to some H. influenzae biogroup aegyptius strains. The hifE(F3031) allele was limited to H. influenzae biogroup aegyptius. Two strains contained one copy of hifE(F3031) and one copy of a variant hifE allele. We determined the nucleotide sequences of four hifE genes from H. influenzae biogroup aegyptius and H. influenzae capsule serotypes a and c. The predicted proteins produced by these genes demonstrated only 35 to 70% identity to the three published HifE proteins from nontypeable H. influenzae, serotype b, and BPF strains. The C-terminal third of the molecules implicated in chaperone binding was the most highly conserved region. Three conserved domains in the otherwise highly variable N-terminal putative receptor-binding region of HifE were similar to conserved portions in the N terminus of Neisseria pilus adhesin PilC. We concluded that two pilus clusters and hifE(F3031) were not specific for BPF-causing H. influenzae, and we also identified portions of HifE possibly involved in binding mammalian cell receptors.
Reversal of Obesity and Insulin Resistance by a Non-Peptidic Glucagon-Like Peptide-1 Receptor Agonist in Diet-Induced Obese Mice (2010)

Boc5 may produce metabolic benefits via multiple synergistic mechanisms and may represent an attractive tool for therapeutic intervention of obesity and diabetes, by means of non-peptidic GLP-1R agonism.
Letter: 755-nm Alexandrite Laser Epilation as an Adjuvant and Primary Treatment for Pilonidal Sinus Disease (2010)

ABBAS, OSSAMA MD*; SIDANI, MUSTAFA MD*; RUBEIZ, NELLY MD*; GHOSN, SAMER MD*; KIBBI, ABDUL GHANI MD* Author Information
A Case of Sex Headache and Vasospasm (2004)

Thunderclap headache (TCH) refers to a severe headache of sudden onset in which pain reaches maximal intensity within seconds or minutes (J Neurol
Distributed power control subject to channel and interference estimation errors (2014)

Perfect estimation of receiver interference power is a fundamental assumption in most distributed power control algorithms. Newer techniques in managing interference through transmit power control rely on local observations of channel information where the obtained information is assumed to be error-free. In this paper, we investigate the performance degradation in distributed power control algorithms due to estimation errors. We present some bounds on the resulted transmit power and signal to interference and noise ratio (SINR) errors due to imperfect estimations. Specifically, we find that for interference-limited scenarios, there is a potential SINR loss of up to 3-dB even for tiny errors in channel state information.
Cavernomes du tronc cérébral: indications opératoires à propos de 7 cas (1992)

info:eu-repo/semantics/nonPublished
Evaluation of liver grafts with warm ischemia and with different cold preservation time in liver transplantation. (2010)

Objective To evaluate the efficacy of liver grafts with warm ischemia and with different cold preservation time in liver transplantation.Methods The clinical data of 154 patients who received liver transplantation at the First Affiliated Hospital of Sun Yat-sen University from January 2006 to December 2007 were retrospectively analyzed.The warm ischemia time of the liver grafts obtained from the non-heart-beating donors was within 10 minutes.According to cold perservation time of the liver grafts,patients were divided into 3 groups:the cold preservation time of the liver grafts was within 8 hours,8-12 hours and above 12 hours in group I(n=58),group Ⅱ(n=62)and group Ⅲ(n=34),respectively.The peak level of alanine aminotransferase(ALT),primary graft dysfunction(PGD)after liver transplantation,acute rejection response,biliary complications,vessel complications,perioperative infections and the survival of liver grafts and recipients among the 3 groups were analyzed via chi-square test,t test and variance analysis.Results No PGD was detected in the 3 groups after liver transplantation.All patients were followed up for 8-32 months.The peak level of ALT,incidence of infection and biliary complication,survival of liver grafts and recipients were(482±357)U/L,12%(7/58),12%(7/58),86%(50/58)and 88%(51/58)in group Ⅰ,and were(1274±608)U/L,29%(10/34),26%(9/34),68%(23/34)and 71%(24/34)in group Ⅲ,with significant difference between the 2 groups(t=5.23,X~2=4.28,6.77,4.51,4.28,P<0.05).The peak level of ALT in group Ⅱ was(953±424)U/L,which was significant higher than(482±357)U/L in group Ⅰ(t=4.76,P＜0.05).Conclusions Liver grafts with a warm ischemia time shorter than 10 minutes could tolerate the injury caused by cold preservation with the maximum time of 12 hours.The incidences of biliary complications and postoperative infections are significantly increased and the survivals of liver grafts and recipients are decreased when the cold preservation time exceeds 12 hours.

Key words: 
Liver transplantation; Non-heart-beating donor; Warm ischemia; Cold preservation
Cellular Basis for the Brugada Syndrome and Other Mechanisms of Arrhythmogenesis Associated With ST-Segment Elevation (1999)

Using arterially perfused wedges of canine right ventricle (RV), we simultaneously recorded transmembrane action potentials from 2 epicardial and 1 endocardial sites, together with unipolar electrograms and a transmural ECG. Loss of the action potential dome in epicardium but not endocardium after exposure to pinacidil (2 to 5 micromol/L), a K(+) channel opener, or the combination of a Na(+) channel blocker (flecainide, 7 micromol/L) and acetylcholine (ACh, 2 to 3 micromol/L) resulted in an abbreviation of epicardial response and a transmural dispersion of repolarization, which caused an ST-segment elevation in the ECG. ACh facilitated loss of the action potential dome, whereas isoproterenol (0.1 to 1 micromol/L) restored the epicardial dome, thus reducing or eliminating the ST-segment elevation. Heterogeneous loss of the dome caused a marked dispersion of repolarization within the epicardium and transmurally, thus giving rise to phase 2 reentrant extrasystole, which precipitated ventricular tachycardia (VT) and ventricular fibrillation (VF). Transient outward current (I(to)) block with 4-aminopyridine (1 to 2 mmol/L) or quinidine (5 micromol/L) restored the dome, normalized the ST segment, and prevented VT/VF. Conclusions-Depression or loss of the action potential dome in RV epicardium creates a transmural voltage gradient that may be responsible for the ST-segment elevation observed in the Brugada syndrome and other syndromes exhibiting similar ECG manifestations. Our results also demonstrate that extrasystolic activity due to phase 2 reentry can arise in the intact wall of the canine RV and serve as the trigger for VT/VF. Our data point to I(to) block (4-aminopyridine, quinidine) as an effective pharmacological treatment.
Power Doppler imaging and resistance index measurement in the evaluation of acute renal transplant rejection (2001)

Neither grading of vascularity on power Doppler images, RI measurement, nor the combination of these methods is an accurate means of detecting renal allograft rejection.
Scalable approaches for path computation (2015)

Optimal and fast approaches for path computation are of paramount importance especially for the path computation elements (PCE) of generalized multi-protocol label switching (GMPLS) networks. To overcome the computational complexity, optimality must be traded for the execution time, enabling scalable computation. This paper considers the typical routing problems addressed by PCE and compares different optimization approaches based on integer linear programming (ILP) formulation and its relaxation, with the objective of assessing optimality and scalability of the approaches.
ISOLATION AND ESTIMATION OF »FREE« OESTROGENS IN HUMAN PLACENTAE (1956)

The principal oestrogens of the human placenta were first isolated by Doisy and his co-workers (Westerfeld et al., 1938, Huffman et al., 1940). Working with more than 400 kg. full-term placentae, these investigators calculated the oestrogen concentration as being 35 μg. oestrone, 38 μg. oestradiol-17β and 140 μg. oestriol per kg. wet tissue. In 1953 a method was described for the separate estimation of »free«. »conjugated« and »protein-bound« oestrogens in early- and full-term placental tissue (Diczfalusy, 1953). By using this method which is dependent on solvent partition, countercurrent distribution and fluorimetric analysis, the average concentration of »free« oestrogens in six full-term placentae was found to be 46.7 μg. oestrone, 3.1 μg. oestradiol-17β and 125.4 μg. oestriol per kg. tissue. Recovery experiments with relatively high amounts of oestrogens added to early placentae indicated an over-all recovery of approximately 70 per cent.
Sympatric chimpanzees and gorillas harbor convergent gut microbial communities (2013)

The gut microbial communities within great apes have been shown to reflect the phylogenetic history of their hosts, indicating codiversification between great apes and their gut microbiota over evolutionary timescales. But because the great apes examined to date represent geographically isolated populations whose diets derive from different sources, it is unclear whether this pattern of codiversification has resulted from a long history of coadaptation between microbes and hosts (heritable factors) or from the ecological and geographic separation among host species (environmental factors). To evaluate the relative influences of heritable and environmental factors on the evolution of the great ape gut microbiota, we assayed the gut communities of sympatric and allopatric populations of chimpanzees, bonobos, and gorillas residing throughout equatorial Africa. Comparisons of these populations revealed that the gut communities of different host species can always be distinguished from one another but that the gut communities of sympatric chimpanzees and gorillas have converged in terms of community composition, sharing on average 53% more bacterial phylotypes than the gut communities of allopatric hosts. Host environment, independent of host genetics and evolutionary history, shaped the distribution of bacterial phylotypes across the Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria, the four most common phyla of gut bacteria. Moreover, the specific patterns of phylotype sharing among hosts suggest that chimpanzees living in sympatry with gorillas have acquired bacteria from gorillas. These results indicate that geographic isolation between host species has promoted the evolutionary differentiation of great ape gut bacterial communities.
Author response: Changes in global and thalamic brain connectivity in LSD-induced altered states of consciousness are attributable to the 5-HT2A receptor (2018)

LSD induces a pattern of changed global brain connectivity characterized by hypo-connectivity in associative areas and hyper-connectivity across sensory and somatomotor areas that is dependent on the serotonin 2A receptor.
Light-Stimulated Electrical Responses from Skin (1966)

When skin is exposed to an intense flash of light, an early electrical response can be detected from its surface. The signals that occur during the first milliseconds after the flash are similar to electrical signals recently observed in the eye from the cell layers containing melanin. Possibly the melanin in skin augments, but does not directly generate, this early electrical response. In addition, a late response, which arises hundreds of milliseconds after the flash, also occurs in skin. Unlike the early response, the late response is sensitive only to violet and shorter wavelengths of light and hence is probably mediated by a pigment other than melanin.
Glycan Microheterogeneity at the PGT135 Antibody Recognition Site on HIV-1 gp120 Reveals a Molecular Mechanism for Neutralization Resistance (2015)

Broadly neutralizing antibodies have been isolated that bind the glycan shield of the HIV-1 envelope spike. One such antibody, PGT135, contacts the intrinsic mannose patch of gp120 at the Asn332, Asn392, and Asn386 glycosylation sites. Here, site-specific glycosylation analysis of recombinant gp120 revealed glycan microheterogeneity sufficient to explain the existence of a minor population of virions resistant to PGT135 neutralization. Target microheterogeneity and antibody glycan specificity are therefore important parameters in HIV-1 vaccine design.