gebhart/patrepeval huggingface dataset:
Matrix-Assisted Laser Desorption Ion Trap Mass Spectrometry:  Efficient Isolation and Effective Fragmentation of Peptide Ions (1996)

Effective analysis of the sequence of peptides using matrix-assisted laser desorption/ionization (MALDI) tandem ion trap mass spectrometry requires efficient mass isolation and the ability to induce extensive sequence-specific fragmentation. The present paper describes a new excitation scheme, which we term red-shifted off-resonance large-amplitude excitation (RSORLAE), that can deposit higher amounts of internal energy in ions than is feasible with conventional resonant excitation. The new method provides an effective means for inducing fragmentation of MALDI-produced peptide ions with m/z values up to 3500. Prior to excitation, it is necessary to isolate ions of interest with high efficiency. We demonstrate that isolation efficiencies of > 95% can be achieved by careful design of the rf scan functions used during ion isolation. In particular, sudden transitions in the amplitude of the rf field (from low to high amplitudes) must be avoided. The combined improvements in the efficiency for ion isolation and the efficacy of ion activation make MALDI tandem ion trap mass spectrometry a practical tool for the characterization of proteins with high sensitivity.
[Effectiveness of beta-hydroxyethylrutoside in patients with varicose veins in pregnancy]. (1995)

Pregnancy is a critical risk for development of varicosis, therefore early detection and treatment are strongly recommended. In our study we examined 51 patients subdivided into three groups. One group underwent physical therapy (cold foot-baths in the morning an in the evening), the other group was administered beta-hydroxyethyl rutosides, and the patients of the third group had appeared only once for examination. Leg circumference and diameter of vein (by sonography) were measured, and the subjective criteria evaluated. In the group of patients who were additionally given drugs, a significant reduction of all parameters was found: leg circumference was reduced by 3% and diameters of veins were reduced by 15% on average, the reduction of the subjective criteria was by 34%. Provided the veins were prevented from further extension through progressive varicosis, apparent beneficial clinical effects can be achieved by administration of beta-hydroxyethyl rutosides.
Lossy Image Compression with Compressive Autoencoders (2020)

We propose a new approach to the problem of optimizing autoencoders for lossy image compression. New media formats, changing hardware technology, as well as diverse requirements and content types create a need for compression algo- rithms which are more flexible than existing codecs. Autoencoders have the po- tential to address this need, but are difficult to optimize directly due to the inherent non-differentiabilty of the compression loss. We here show that minimal changes to the loss are sufficient to train deep autoencoders competitive with JPEG 2000 and outperforming recently proposed approaches based on RNNs. Our network is furthermore computationally efficient thanks to a sub-pixel architecture, which makes it suitable for high-resolution images. This is in contrast to previous work on autoencoders for compression using coarser approximations, shallower archi- tectures, computationally expensive methods, or focusing on small image.
Integrated Functional, Gene Expression and Genomic Analysis for the Identification of Cancer Targets (2009)

The majority of new drug approvals for cancer are based on existing therapeutic targets. One approach to the identification of novel targets is to perform high-throughput RNA interference (RNAi) cellular viability screens. We describe a novel approach combining RNAi screening in multiple cell lines with gene expression and genomic profiling to identify novel cancer targets. We performed parallel RNAi screens in multiple cancer cell lines to identify genes that are essential for viability in some cell lines but not others, suggesting that these genes constitute key drivers of cellular survival in specific cancer cells. This approach was verified by the identification of PIK3CA, silencing of which was selectively lethal to the MCF7 cell line, which harbours an activating oncogenic PIK3CA mutation. We combined our functional RNAi approach with gene expression and genomic analysis, allowing the identification of several novel kinases, including WEE1, that are essential for viability only in cell lines that have an elevated level of expression of this kinase. Furthermore, we identified a subset of breast tumours that highly express WEE1 suggesting that WEE1 could be a novel therapeutic target in breast cancer. In conclusion, this strategy represents a novel and effective strategy for the identification of functionally important therapeutic targets in cancer.
Presence of Acetyl Coenzyme A (CoA) Carboxylase and Propionyl-CoA Carboxylase in Autotrophic Crenarchaeota and Indication for Operation of a 3-Hydroxypropionate Cycle in Autotrophic Carbon Fixation (1999)

The pathway of autotrophic CO2 fixation was studied in the phototrophic bacterium Chloroflexus aurantiacus and in the aerobic thermoacidophilic archaeon Metallosphaera sedula. In both organisms, none of the key enzymes of the reductive pentose phosphate cycle, the reductive citric acid cycle, and the reductive acetyl coenzyme A (acetyl-CoA) pathway were detectable. However, cells contained the biotin-dependent acetyl-CoA carboxylase and propionyl-CoA carboxylase as well as phosphoenolpyruvate carboxylase. The specific enzyme activities of the carboxylases were high enough to explain the autotrophic growth rate via the 3-hydroxypropionate cycle. Extracts catalyzed the CO2-, MgATP-, and NADPH-dependent conversion of acetyl-CoA to 3-hydroxypropionate via malonyl-CoA and the conversion of this intermediate to succinate via propionyl-CoA. The labelled intermediates were detected in vitro with either 14CO2 or [14C]acetyl-CoA as precursor. These reactions are part of the 3-hydroxypropionate cycle, the autotrophic pathway proposed for C. aurantiacus. The investigation was extended to the autotrophic archaea Sulfolobus metallicus and Acidianus infernus, which showed acetyl-CoA and propionyl-CoA carboxylase activities in extracts of autotrophically grown cells. Acetyl-CoA carboxylase activity is unexpected in archaea since they do not contain fatty acids in their membranes. These aerobic archaea, as well as C. aurantiacus, were screened for biotin-containing proteins by the avidin-peroxidase test. They contained large amounts of a small biotin-carrying protein, which is most likely part of the acetyl-CoA and propionyl-CoA carboxylases. Other archaea reported to use one of the other known autotrophic pathways lacked such small biotin-containing proteins. These findings suggest that the aerobic autotrophic archaea M. sedula, S. metallicus, and A. infernus use a yet-to-be-defined 3-hydroxypropionate cycle for their autotrophic growth. Acetyl-CoA carboxylase and propionyl-CoA carboxylase are proposed to be the main CO2 fixation enzymes, and phosphoenolpyruvate carboxylase may have an anaplerotic function. The results also provide further support for the occurrence of the 3-hydroxypropionate cycle in C. aurantiacus.
PERIOD1-Associated Proteins Modulate the Negative Limb of the Mammalian Circadian Oscillator (2005)

The clock proteins PERIOD1 (PER1) and PERIOD2 (PER2) play essential roles in a negative transcriptional feedback loop that generates circadian rhythms in mammalian cells. We identified two PER1-associated factors, NONO and WDR5, that modulate PER activity. The reduction of NONO expression by RNA interference (RNAi) attenuated circadian rhythms in mammalian cells, and fruit flies carrying a hypomorphic allele were nearly arrhythmic. WDR5, a subunit of histone methyltransferase complexes, augmented PER-mediated transcriptional repression, and its reduction by RNAi diminished circadian histone methylations at the promoter of a clock gene.
Vehicle detection video through image processing: the Autoscope system (1991)

Recent worldwide developments concerning the use of vehicle detection for wireless large-scale data collection and implementation of advanced traffic control and management schemes such as vehicle guidance/navigation are briefly discussed, and the system developed in the US, Autoscope, is described. Early work on Autoscope, leading to its present advantages over other emerging devices, and recent progress, such as preproduction line prototype development, field testing, and plans for extensive field validation and verification, are examined. The aforementioned plans include two large demonstration projects recently initiated in Minneapolis. In the first project, Autoscope will be used for incident detection over a section of Interstate 394. The second project involves implementation of the machine vision system at a signalized intersection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Radioiodination and biological distribution of a new s‐triazine derivative for tumor uptake evaluation (2018)

A newly synthesized s-triazine derivative 1,1',1″-(((1,3,5-triazine-2,4,6-triyl) tris (azanediyl)) tris (benzene-4,1-diyl))tris (ethan-1-one), (1), was synthesized as a part of an ongoing research for development of novel s-triazine-based radiopharmaceuticals. In-vitro cell viability assay against different human cancer cell lines showed very promising inhibitory activity of the synthesized compound. This finding encouraged the radioiodination of 1 to study the degree of its localization in tumor site for evaluating the possibility of its use as a tumor imaging agent. The biodistribution study showed good localization of the radioiodinated derivative 2 at tumor site following i.v. administration in solid tumor-bearing mice. Finally, in a trial to understand the mechanism of the anticancer effect exerted by 1, a target prediction study and a docking study were performed. The results of the first study showed that focal adhesion kinase is a possible target for compound 1 and the docking study confirmed successful binding of both compound 1 and its radioiodinated derivative 2 to the binding site of focal adhesion kinase. As a conclusion, the results of this study suggest that, compound 2 could be used as a potential agent for tumor imaging after preclinical trials.
Anti-caveolin-1 Antibodies As Anti-Prostate Cancer Therapeutics (2012)

Caveolae are critical cell surface structures important in coordinated cell signaling and endocytosis. One of the major proteins of caveolae is caveolin 1 (Cav-1). Cellular levels of Cav-1 are associated with cancer progression. In prostate cancer cells, levels of Cav-1 are positively correlated with tumor progression and metastasis. Cav-1 can be secreted by prostate cancer cells into the microenvironment and triggers proliferation and anti-apoptosis of the tumor and tumor endothelial cells. Clinical studies have shown increased serum Cav-1 levels in patients with poor prognosis. In tissue culture and animal model experiments, blocking secreted Cav-1 by polyclonal antibodies inhibits tumor cell growth. Cav-1 is therefore a potential therapeutic target for prostate cancer treatment. In this study, we used Cav-1 knock-out mice as hosts to produce monoclonal anti-Cav-1 antibodies. A total of 11 hybridoma cell lines were selected for their ability to produce antibodies that bound GST-Cav-1 but not GST on glutathione-coated ELISA plates. Further screening with ELISAs using GST-Cav-1 fragments on GSH-coated plates classified these antibodies into four groups: N1-31 with five antibodies binds the far N-terminus between amino acids 1 and 31; N32-80 with three antibodies binds between amino acids 32 and 80; CSD with two antibodies potentially bind the scaffolding domain (amino acids 80-101); and Cav-1-C with 1 antibody binds parts of the C-terminal half. Binding affinities (Kd) of these antibodies to soluble Cav-1 ranged from 10(-11) to 10(-8) M. Binding competition experiments revealed that these antibodies recognized a total of six different epitopes on Cav-1. Potency of these antibodies to neutralize Cav-1-mediated signaling pathways in cultured cells and in animal models will be tested. A selected monoclonal antibody will then be humanized and be further developed into a potential anti-prostate cancer therapeutic.
Cleavage anomalies in early human embryos and survival after prolonged culture in-vitro (2000)

This study examines the relationship between common morphological anomalies of cleaving embryos and their ability to form apparently normal blastocysts in vitro. The impact of cleavage rate, fragmentation, and multinucleation on compaction, cavitation, along with inner cell mass and trophectoderm formation has been assessed. The study population consisted of 102 patients who elected or were selected to have a day 5 embryo transfer. Clinical pregnancy and implantation rates were 66.7 and 49% respectively. Slow and fast cleavage had a significant negative association with normal blastocyst formation. Only 13.8% (67/484) of embryos with <7 cells and 27.5% (25/91) of those with >9 cells on day 3 formed blastocysts with apparently normal morphology, compared to 41.9% (252/602) with 7-9 cells on day 3 (P < 0.001). Fragmentation had a negative impact on normal blastocyst formation. Embryos with >15% fragmentation formed normal blastocysts at a significantly lower rate (46/279; 16.5%) than embryos with 0-15% fragmentation (311/935; 33.3%) (P < 0. 001). Furthermore, the pattern of fragmentation was associated with blastocyst formation. Type IV fragmentation led to a significant reduction in blastocyst formation (25/170 or 14.7%), compared to types I, II and III which performed much better (38.6, 32.9 and 32.4% respectively). Only 15.9% (22/138) of embryos with one or more multinucleate cells on day 2 and/or 3 formed normal blastocysts compared with 31.9% (335/1051) (P < 0.001) of those without multinucleation. Collectively, the data suggest that cleavage anomalies, some of which do not preclude development after short-term culture, may reduce the developmental competence of embryos after prolonged culture.
Tyrosine kinase inhibitors reverse type 1 diabetes in nonobese diabetic mice (2008)

The recent development of small-molecule tyrosine kinase (TK) inhibitors offers increasing opportunities for the treatment of autoimmune diseases. In this study, we investigated the potential of this new class of drugs to treat and cure type 1 diabetes (T1D) in the NOD mouse. Treatment of prediabetic and new onset diabetic mice with imatinib (Gleevec) prevented and reversed T1D. Similar results were observed with sunitinib (Sutent), an additional approved multikinase inhibitor, suggesting that the primary target of imatinib, c-Abl, was not essential in blocking disease in this model. Additional studies with another TK inhibitor, PLX647 (targeting c-Kit and c-Fms) or an anti-c-Kit mAb showed only marginal efficacy whereas a soluble form of platelet-derived growth factor receptor (PDGFR), PDGFRbetaIg, rapidly reversed diabetes. These findings strongly suggest that inhibition of PDGFR is critical to reverse diabetes and highlight a crucial role of inflammation in the development of T1D. These conclusions were supported by the finding that the adaptive immune system was not significantly affected by imatinib treatment. Finally, and most significantly, imatinib treatment led to durable remission after discontinuation of therapy at 10 weeks in a majority of mice. Thus, long-term efficacy and tolerance is likely to depend on inhibiting a combination of tyrosine kinases supporting the use of selective kinase inhibitors as a new, potentially very attractive approach for the treatment of T1D.
Reinvigorating exhausted HIV-specific T cells via PD-1–PD-1 ligand blockade (2006)

The programmed death (PD)-1-PD-1 ligand (PD-L) pathway, which is part of the B7-CD28 family, consists of the PD-1 receptor and its two ligands PD-L1 and PD-L2. Engagement of PD-1 by its ligands inhibits immune responses, and recent work has shown that PD-1 is highly expressed on exhausted T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Blockade of this pathway reinvigorates the exhausted T cells, allowing them to expand and produce effector cytokines, raising the issue of whether this pathway has been exploited by a variety of viruses during chronic infection. New studies now extend these observations to HIV infection and human disease.
Lactoferrin gene promoter: structural integrity and nonexpression in HL60 cells (1992)

Lactoferrin is a member of the transferrin family of iron-binding proteins. It is found in several glandular epithelial tissues and human neutrophils, where it is localized to secondary granules. To examine the mechanisms controlling lactoferrin gene expression in neutrophils and defects in its expression in acute leukemia, we have cloned a lactoferrin cDNA from a chronic myelogenous leukemia library, and used it to obtain genomic clones representing the chromosomal lactoferrin gene. Using polymerase chain reaction, primer extension, and S1 analysis, we have identified the 5′ end of the lactoferrin mRNA. We have defined a putative promoter region for the gene, and characterized its first two exons. In addition, we have examined the structure of these regions in DNA from HL60 cells. HL60 is a leukemic cell line that undergoes phenotypic neutrophil maturation on exposure to dimethyl sulfoxide (DMSO). However, the cells cannot be induced to express any secondary granule protein genes. We have shown that the 5′ end of the lactoferrin gene, including the putative promoter region, is entirely normal in HL60. By Northern analysis, nuclear run-on studies, and primer extension assays we have shown that the gene is not transcribed in DMSO-induced HL60 cells. This supports the hypothesis that the defect in HL60 is an abnormality in the production or activity of a transacting regulator of lactoferrin gene expression.
Algorithms for data stream systems (2003)

In a growing number of information-processing applications, data takes the form of “continuous data streams” rather than traditional stored databases. These applications share several distinguishing features like the need for real time analysis, huge volumes of data, and unpredictable and bursty data arrivals. Application areas include network-traffic monitoring, sensor networks, and many more. For such applications, it is not feasible to simply load the arriving data into a traditional database management system (DBMS) or load it into main memory, and operate on it there. The failure to use these solutions precludes random access to data elements that is assumed in the traditional main memory model of computation. This leads us to the data stream model of computation, in which some or all of the input data that is to be operated on, is not available for random access from disk or memory, but rather arrives as one or more continuous data streams . Using a small amount of main memory and small update time, we are required to give continuous answers to queries posed over data streams. 
This thesis considers two sets of issues in the area of data-stream computation: algorithms and theory, and techniques for runtime resource allocation in systems designed for stream computations. 
In the area of algorithms we present space- and time-efficient algorithms for a number of problems in the sliding-window model. In this model only the last N elements, where N is the window size, are relevant to gathering statistics or answering queries. We also propose the computation of Hamming norms over data streams, which is a more general problem than the well-studied distinct value estimation problem, and present efficient algorithms for Hamming-norm computation in the presence of inserts and deletes. 
In the area of stream-systems we study two runtime resource allocation problems: operator scheduling and load shedding. We develop an operator-scheduling strategy called Chain that minimizes the total memory requirement of the system. We then study load shedding for aggregations queries, and present optimal algorithms that minimize the inaccuracy in query answers given a load constraint. We present a thorough experimental evaluation for both techniques.
Clade, Country and Region-specific HIV-1 Vaccines: Are they necessary? (2005)

Today, scientists are often encouraged to custom-design vaccines based on a particular country or clade. Here, we review the scientific literature and then suggest that the overwhelming endeavor to produce a unique vaccine for every world region or virus subtype may not be necessary.
Dendritic Cells (2003)

The immune system is controlled by dendritic cells (DCs). Just as lymphocytes comprise different subsets, DCs comprise several subsets that differentially control lymphocyte function. In humans, the myeloid pathway includes Langerhans cells (LCs) and interstitial DCs (intDCs). While both subsets produce IL-12, only intDCs make IL-10 and induce B cell differentiation. Another pathway includes plasmacytoid DCs, which promptly secrete large amounts of IFN-alpha/beta viral encounter. Thus, insights into in vivo DC functions are important to understand the launching and modulation of immunity.
Temporal Event Sequence Simplification (2013)

Electronic Health Records (EHRs) have emerged as a cost-effective data source for conducting medical research. The difficulty in using EHRs for research purposes, however, is that both patient selection and record analysis must be conducted across very large, and typically very noisy datasets. Our previous work introduced EventFlow, a visualization tool that transforms an entire dataset of temporal event records into an aggregated display, allowing researchers to analyze population-level patterns and trends. As datasets become larger and more varied, however, it becomes increasingly difficult to provide a succinct, summarizing display. This paper presents a series of user-driven data simplifications that allow researchers to pare event records down to their core elements. Furthermore, we present a novel metric for measuring visual complexity, and a language for codifying disjoint strategies into an overarching simplification framework. These simplifications were used by real-world researchers to gain new and valuable insights from initially overwhelming datasets.
A Microjet Array Cooling System for Thermal Management of High-Brightness LEDs (2007)

In this paper, a microjet-based cooling system is proposed for the thermal management of high-power light-emitting diodes (LEDs). Preliminary experimental investigation and numerical simulation on such an active cooling system are conducted. In the experiment investigation, thermocouples are packaged with LED chips to measure the temperature and evaluate the cooling performance of the proposed system. The experimental results demonstrate that the microjet-based cooling system works well. For a 2 times 2 LED chip array, when the input power is 5.6 W and the environment temperature is 28degC, without any active cooling techniques, the temperature of 2 times 2 LED chip array substrate reaches 72degC within 2 min and will continue to increase sharply. However, by using the proposed cooling system, when the flow rate of micropump is 9.7 mL/s, the maximum LED substrate temperature measured by the thermocouples will remain stable at about 36.7degC. As for the numerical optimization, the comparison between the simulation and experimental results is presented to confirm the feasibility of the simulation model. By using the simulation model, the effects of microjet diameter, top cavity height, micropump flow rate, and jet device material on system performance are numerically studied. According to the preliminary test and numerical optimization, an optimized microjet cooling system is fabricated and applied in thermal management of a 220-W LED lamp. The temperature test demonstrates that the cooling system has good performance.