gebhart/patrepeval huggingface dataset:
Structural analysis of a peptide-HLA class II complex: identification of critical interactions for its formation and recognition by T cell receptor (1989)

An assay for the binding of peptides to major histocompatibility complex (MHC) class II proteins on the surface of cells has been used to determine the relative importance of the amino acids composing an influenza haemagglutinin T cell determinant in binding. The important contact residues were identified by the effect substitution of each residue with biotinylated lysine had on the ability of the peptide to bind. The spacing of the critical residues within the peptide sequence was consistent with the central core, of approximately eight amino acids, adopting a helical conformation. The terminal residues were less constrained and might not be part of a regular conformation. Increasing the helical propensity of the determinant, by simply acetylating and amidating the peptide, resulted in an analogue that was able to stimulate a specific T cell clone at significantly lower concentrations than the natural sequence. A potential location for the peptide in the binding site was postulated based on the presence of complementary amino acids in the class II molecule and supported by screening a large number of peptide analogues for their ability either to bind the restriction element or to stimulate T cell proliferation.
NONO and RALY proteins are required for YB-1 oxaliplatin induced resistance in colon adenocarcinoma cell lines (2011)

These results suggest knocking down NONO or RALY significant counteracts oxaliplatin resistance in colorectal cancers overexpressing the YB-1 protein.
Laser-Induced Damage in Dielectrics with Nanosecond to Subpicosecond Pulses (1995)

We report extensive measurements of damage thresholds for fused silica and calcium fluoride at 1053 and 526 nm for pulse durations $\ensuremath{\tau}$ ranging from 270 fs to 1 ns. Qualitative differences in the morphology of damage and a departure from the diffusion-dominated ${\ensuremath{\tau}}^{1/2}$ scaling indicate that damage results from plasma formation and ablation for $\ensuremath{\tau}\ensuremath{\le}10$ ps and from conventional melting and boiling for $\ensuremath{\tau}&gt;100$ ps. A theoretical model based on electron production via multiphoton ionization, Joule heating, and collisional (avalanche) ionization is in good agreement with experimental results.
In vivo adjuvant effect of interleukins 5 and 6 on rat tear IgA antibody responses. (1991)

Interleukins 5 and 6 have previously been shown to exhibit IgA-enhancing activity in vitro. This study investigated the effect of IL-5 and IL-6 on antigen-specific tear IgA antibody responses in vivo. Rats were given primary and secondary immunizations by the ocular-topical (OT) route with either antigen (DNP-Pn) alone or antigen plus IL-5 and IL-6 (IL-5/6). Antigen was administered for the first 3 days of each stimulation cycle and lymphokines (50 units of each lymphokine/eye/day) or control media for the first 7 days of the primary and secondary immunizations. Co-administration of antigen with IL-5/6 markedly enhanced (approximately three-fold) the secondary tear IgA anti-DNP antibody response in the lymphokine-treated group. Enhanced tear IgA antibody responses were maintained in the lymphokine-treated group following a tertiary immunization in the absence of IL-5/6. There was no apparent effect on the total tear IgA levels in either group of animals. Ocular topical immunization also elicited secondary and tertiary serum IgG antibody responses which were not affected by the administration of IL-5/6. Neither secondary nor tertiary serum IgM antibody responses were detected in either group of animals. These data indicate that IL-5 and IL-6 are able to augment tear IgA antibody responses in vivo. That the enhancement was maintained following a subsequent antigenic challenge in the absence of the lymphokines suggests a potential therapeutic application for lymphokines in augmenting IgA responses at mucosal surfaces.
HAUSP is Required for p53 Destabilization (2004)

p53 ubiquitination is the principal mechanism by which p53 levels are regulated in the cell. HAUSP (also known as USP7) has been proposed to serve as a substrate-specific deubiquitinase of p53, and an increase in p53 levels was reported upon overexpression of HAUSP. We have disrupted the HAUSP genomic locus by homologous recombination and shown that HAUSP ablation results in a phenotype opposite to that predicted. Rather than decreasing p53 levels associated with increased p53 ubiquitination, the absence of HAUSP resulted in p53 accumulation accompanied by decreased p53 ubiquitination. The p53 protein in HAUSP-deficient cells was active, as assessed by the induction of its transcriptional targets and growth arrest. The basis for this phenotype was traced to the increased ubiquitination of MDM2, a negative regulator of p53 levels. These results demonstrate that MDM2, rather than p53, is the substrate for HAUSP under physiologic conditions and document a fascinating and unexpected twist to the regulation of the p53/MDM2 axis.
Delving Deeper into Convolutional Networks for Learning Video Representations (2015)

We propose an approach to learn spatio-temporal features in videos from intermediate visual representations we call "percepts" using Gated-Recurrent-Unit Recurrent Networks (GRUs).Our method relies on percepts that are extracted from all level of a deep convolutional network trained on the large ImageNet dataset. While high-level percepts contain highly discriminative information, they tend to have a low-spatial resolution. Low-level percepts, on the other hand, preserve a higher spatial resolution from which we can model finer motion patterns. Using low-level percepts can leads to high-dimensionality video representations. To mitigate this effect and control the model number of parameters, we introduce a variant of the GRU model that leverages the convolution operations to enforce sparse connectivity of the model units and share parameters across the input spatial locations. We empirically validate our approach on both Human Action Recognition and Video Captioning tasks. In particular, we achieve results equivalent to state-of-art on the YouTube2Text dataset using a simpler text-decoder model and without extra 3D CNN features.
MS characterization of multiple forms of alpha‐amylase in human saliva (2005)

Alpha-amylase is a major and well-characterized component of human saliva. Recent proteomic studies suggested that this protein could be observed in more than twenty spots on 2-D gels of salivary proteins. The aim of this work was to investigate this unexpected redundancy. 2-D gel electrophoresis was combined with systematic MALDI-TOF MS analysis. More than 140 protein spots identifying the alpha-amylase were shown to constitute a stable but very complex pattern. Careful analysis of mass spectra and simultaneous hierarchical clustering of the observed peptides and of the electrophoretic features of spots allowed one to define three major groups. A main class grouping 90 spots was shown to correspond to full length alpha-amylases that can be assumed to include isoforms and post-translationally modified forms, a subset of this class being demonstrated to be N-glycosylated. A second group included short alpha-amylases that are differently truncated in a non-random manner, very likely in the oral cavity. The last class grouped alpha-amylase forms showing both the N- and C-terminal sequences of the enzyme but displaying a molecular weight that was up to 50% lower than that of the native protein. It is speculated that the last group of alpha-amylase spots could correspond to proteins submitted to internal deletions prior to the secretion.
[Design and construction of artificial biological systems for complex natural products biosynthesis]. (2013)

Natural products (NPs) are important drug pools for human disease prevention and treatment. The great advances in synthetic biology have greatly revolutionized the strategies of NPs development and production. This review entitled with design and construction of artificial biological systems for complex NPs biosynthesis, mainly introduced the progresses in artificial design of synthetic biological parts, naturally mining novel synthetic parts of NPs, the assembly & adaption of the artificial biological modules & systems.
Sequence Analysis and Expression of the Host-protective Immunogen VP2 of a Variant Strain of Infectious Bursal Disease Virus Which Can Circumvent Vaccination with Standard Type I Strains (1991)

The host-protective antigen VP2 of a variant strain of infectious bursal disease virus (IBDV) which emerged from a vaccinated flock and is able to circumvent vaccination with classic type I strains of IBDV, was cloned and its nucleotide sequence determined. Virus-neutralizing monoclonal antibodies (MAbs) raised against the Australian 002-73 strain of IBDV did not react or reacted only very weakly with the expression product of the variant virus. The deduced amino acid sequence of VP2 from the variant strain differed in 17 residues from that of the Australian strain and in eight positions from a consensus sequence compiled from six type I strains of IBDV. All the amino acid changes mapped within the central, variable region of VP2, which forms the conformational epitope recognized by virus-neutralizing MAbs. Changes in the two hydrophilic regions at either end of this fragment were unique to the variant virus and were crucial for its ability to escape the virus-neutralizing antibodies induced by vaccination with a standard type I vaccine.
Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival (2011)

High-throughput biological data, whether generated as sequencing, transcriptional microarrays, proteomic, or other means, continues to require analytic methods that address its high dimensional aspects. Because the computational part of data analysis ultimately identifies shape characteristics in the organization of data sets, the mathematics of shape recognition in high dimensions continues to be a crucial part of data analysis. This article introduces a method that extracts information from high-throughput microarray data and, by using topology, provides greater depth of information than current analytic techniques. The method, termed Progression Analysis of Disease (PAD), first identifies robust aspects of cluster analysis, then goes deeper to find a multitude of biologically meaningful shape characteristics in these data. Additionally, because PAD incorporates a visualization tool, it provides a simple picture or graph that can be used to further explore these data. Although PAD can be applied to a wide range of high-throughput data types, it is used here as an example to analyze breast cancer transcriptional data. This identified a unique subgroup of Estrogen Receptor-positive (ER(+)) breast cancers that express high levels of c-MYB and low levels of innate inflammatory genes. These patients exhibit 100% survival and no metastasis. No supervised step beyond distinction between tumor and healthy patients was used to identify this subtype. The group has a clear and distinct, statistically significant molecular signature, it highlights coherent biology but is invisible to cluster methods, and does not fit into the accepted classification of Luminal A/B, Normal-like subtypes of ER(+) breast cancers. We denote the group as c-MYB(+) breast cancer.
Sleep-disordered breathing in children (1998)

The first series of children with obstructive sleep apnoea syndrome was reported in 1976. Later it became apparent that children may have breathing disorders during sleep without frank apnoea or 'hypopnoeas'. This pattern could be detected by measuring the oesophageal pressure. This led to the concept of sleep-disordered breathing as a spectrum that combines obstructive sleep apnoea syndrome and the upper airway resistance syndrome. Studies that do not take into account this spectrum may misclassify symptomatic patients as 'primary snorers'. The exact prevalence of sleep-disordered breathing in children is unknown but may be as high as 11%. There is a familial predisposition to sleep-disordered breathing. Nasal obstruction and mouth breathing influence facial growth, which may further lead to difficulty in breathing while asleep. Symptoms include an increase in total sleep time, nonspecific behavioural difficulties, hyperactivity, irritability, bed-wetting and morning headaches. Clinical signs include failure to thrive, increased respiratory effort with nasal flaring and suprasternal or intercostal retractions. Also, abnormal paradoxical inward motion of the chest may occur during sleep. Excessive daytime sleepiness and obesity are not always present. Untreated children may develop cardiovascular complications. The condition is treatable with continuous or bilevel positive airway pressure, and may be cured with surgery.
Vincristine sulfate liposomal injection for acute lymphoblastic leukemia (2013)

Vincristine (VCR) is one of the most extensively used cytotoxic compounds in hemato-oncology. VCR is particularly important for the treatment of acute lymphoblastic leukemia (ALL), a disease that accounts for approximately one-third of all childhood cancer diagnoses. VCR's full therapeutic potential has been limited by dose-limiting neurotoxicity, classically resulting in autonomic and peripheral sensory-motor neuropathy. In the last decade, however, the discovery that liposomal encapsulation of chemotherapeutics can modulate the pharmacokinetic characteristics of a compound has stimulated much interest in liposomal VCR (vincristine sulfate liposomal injection [VSLI]) formulations for the treatment of ALL and other hematological malignancies. Promising data from recent clinical trials investigating VSLI in adults with ALL resulted in US Food and Drug Administration approval for use in patients with Philadelphia chromosome (t[9;22]/BCR-ABL1) (Ph)-negative (Ph-) disease. Additional clinical trials of VSLI in adults and children with both Ph-positive (Ph+) and Ph- ALL are ongoing. Here we review the preclinical and clinical experience to date with VSLI for ALL.
A Recommended Numbering Scheme for Influenza A HA Subtypes (2014)

Comparisons of residues between sub-types of influenza virus is increasingly used to assess the zoonotic potential of a circulating strain and for comparative studies across subtypes. An analysis of N-terminal cleavage sites for thirteen subtypes of influenza A hemagglutinin (HA) sequences, has previously been described by Nobusawa and colleagues. We have expanded this analysis for the eighteen known subtypes of influenza. Due to differences in the length of HA, we have included strains from multiple clades of H1 and H5, as well as strains of H5 and H7 subtypes with both high and low pathogenicity. Analysis of known structures of influenza A HA enables us to define amino acids which are structurally and functionally equivalent across all HA subtypes using a numbering system based on the mature HA sequence. We provide a list of equivalences for amino acids which are known to affect the phenotype of the virus.
Performance evaluation of a cellular base station multibeam antenna (1997)

Experimental test results are used to determine the performance that can be achieved from a multibeam antenna array, with fixed-beam azimuths, relative to a traditional dual-diversity three-sector antenna configuration. The performance tradeoffs between the hysterisis level, switching time, and gain improvement for a multibeam antenna are also examined. The multibeam antenna uses selection combining to switch the signals from the two strongest directional beams to the base station's main and diversity receivers. To assess the impact of beamwidth on overall system performance, the following two multibeam antennas were tested: a 12-beam 30/spl deg/ beamwidth array and a 24-beam 15/spl deg/ beamwidth array. Both multibeam antennas were field-tested in typical cellular base station sites located in heavy urban and light urban environments. Altogether, the system performance is evaluated by investigating three fundamental aspects of multibeam antenna behavior. First, the relative powers of the signals measured in each directional beam of the multibeam antenna are characterized. Then, beam separation statistics for the strongest two signals are examined. Gain improvements achievable with a multibeam antenna compared to the traditional sector configuration are determined in the second phase of the analysis. Results indicate that in excess of 5 dB of gain enhancement can be achieved with a 24-beam base station antenna in a cellular mobile radio environment. Finally, the effects of hysterisis level and switching time are characterized based on gain reductions relative to a reference case with no hysterisis and a 0.5-s switching decision time. Useful approximations are developed for the gain effects associated with varying hysterisis levels and switching times. The resulting design curves and empirical rules allow engineers to quantify multibeam antenna performance while making appropriate tradeoffs for parameter selection.
Two Cases of Renal Cell Carcinoma Harboring a Novel STRN-ALK Fusion Gene (2016)

Anaplastic lymphoma kinase (ALK) translocation renal cell carcinomas (RCCs) have been reported by several independent groups in recent times. The clinical behavior and histopathologic characteristics of these carcinomas are not fully understood because of the paucity of cases reported. Here, we describe 2 cases of RCC harboring a novel striatin (STRN)-ALK fusion. The first case was a 33-year-old woman with no sickle cell trait who underwent nephrectomy for right renal mass and had late recurrence in para-aortic lymph nodes twice 10 and 12 years after initial surgery. After the second recurrence, she was carefully observed without any treatment. Twenty-six years after the initial nephrectomy, the second para-aortic lymphadenectomy was performed, and gastrectomy was performed for newly developed primary gastric cancer. The resected para-aortic lymph nodes were largely replaced by metastatic carcinoma. The second case was a 38-year-old man with no sickle cell trait who underwent cytoreductive nephrectomy followed by sunitinib therapy for metastatic RCC. In both cases, the tumor showed solid, papillary, tubular, and mucinous cribriform structures. Psammoma bodies were occasionally seen in the stroma. Tumor cells had a large nucleus and prominent nucleoli with predominantly eosinophilic cytoplasm. Rhabdoid cells and signet-ring cells were also observed. Intracytoplasmic mucin deposition and background mucinous stroma were confirmed. In the second case, tumor necrosis was seen in some areas. Tumor cells exhibited diffuse positive staining for ALK in both cases. ALK translocation was confirmed by fluorescent in situ hybridization, and further gene analysis revealed a STRN-ALK fusion. These cases provide great insights into ALK translocation RCCs.
Renal tubular responses to low-dose infusion of angiotensin II in type 1 diabetes mellitus; relation to chronic glycaemic control (1994)

Renal responses to low-dose infusion of angiotensin II (ANGII, 1.25 and 2.5 ng.kg-1 min-1) were examined in 15 patients with type 1 diabetes and in 10 control subjects after pretreatment with lithium carbonate (750 mg, 20 mmol). Mean arterial pressure rose during ANGII infusion in both groups. The renal haemodynamic response to angiotensin II was not abnormal in the diabetic patients. Absolute proximal reabsorption of sodium was increased at baseline in the diabetic group, and fell during ANGII. Fractional lithium excretion was reduced in the diabetic patients at baseline (P < 0.05), and the fall in fractional lithium excretion during ANGII was less than in the control group (P = 0.012). In the diabetic group correlations existed between glycated haemoglobin and baseline glomerular filtration rate (P < 0.05), baseline fractional lithium excretion (P = 0.03), and the fall in fractional lithium excretion during angiotensin II infusion (P = 0.013). There was no correlation between glycated haemoglobin and absolute lithium clearance. Some indices of sodium reabsorption by the proximal renal tubule in diabetic patients correlate with prevailing chronic glycaemic control, largely reflecting changes in glomerular filtration rate. Reduced fractional proximal tubular responsiveness to exogenous angiotensin II is consistent with a role for endogenous angiotensin II as one mediator of increased tubular reabsorption of sodium in type 1 diabetes, but the data does not exclude alternative mechanisms.
Distributed computing in robotics and automation (2002)

The pervasive introduction of the Internet into robotics and automation systems pushes forward an evolution that began when the computer was introduced in the enterprise in the middle of the last century, and that continued. with the interconnection of shop-floor workstations in local networks in the 1980s. Today, the Internet represents a challenge both for research and development in the area of distributed robotics and automation. In order to gain a better understanding and evaluation of results in distributed computing the paper classifies the most promising technological approaches, provides examples of how they are applied in robotics and automation, and discusses available standards and commercial solutions.
Expanding the scope of the ATIS task (1994)

The Air Travel Information System (ATIS) domain serves as the common evaluation task for ARPA spoken language system developers. To support this task, the Multi-Site ATIS Data COllection Working group (MADCOW) coordinates data collection activities. This paper describes recent MADCOW activities. In particular, this paper describes the migration of the ATIS task to a richer relational database and development corpus (ATIS-3) and describes the ATIS-3 corpus. The expanded database, which includes information on 46 US and Canadian cities and 23,457 flights, was released in the fall of 1992, and data collection for the ATIS-3 corpus began shortly thereafter. The ATIS-3 corpus now consists of a total of 8297 released training utterances and 3211 utterances reserved for testing, collected at BBN, CMU, MIT, NIST and SRI. 2906 of the training utterances have been annotated with the correct information from the database. This paper describes the ATIS-3 corpus in detail, including breakdowns of data by type (e.g. context-independent, context-dependent, and unevaluable)and variations in the data collected at different sites. This paper also includes a description of the ATIS-3 database. Finally, we discuss future data collection and evaluation plans.
Cancer-Related Fatigue: A Brief Overview of Current Nursing Perspectives and Experiences (2008)

Cancer-related fatigue (CRF) has often been called the "sixth vital sign" and was the focus of a symposium at the Oncology Nursing Society's 32nd Annual Congress, where nurses discussed CRF's impact on patients. Despite this dialogue, current nursing perspectives and practice still need to be determined. The definition of CRF as a multidimensional symptom will be considered in this article. CRF may create psychological, functional, cognitive, and socioeconomic issues in patients. Challenges for effective management will be considered.