gebhart/patrepeval huggingface dataset:
Integrative analysis correlates donor transcripts to recipient autoantibodies in primary graft dysfunction after lung transplantation (2010)

Up to one in four lung-transplanted patients develop pulmonary infiltrates and impaired oxygenation within the first days after lung transplantation. Known as primary graft dysfunction (PGD), this condition increases mortality significantly. Complex interactions between donor lung and recipient immune system are the suspected cause. We took an integrative, systems-level approach by first exploring whether the recipient's immune response to PGD includes the development of long-lasting autoreactivity. We next explored whether proteins displaying such differential autoreactivity also display differential gene expression in donor lungs that later develop PGD compared with those that did not. We evaluated 39 patients from whom autoantibody profiles were already available for PGD based on chest radiographs and oxygenation data. An additional nine patients were evaluated for PGD based on their medical records and set aside for validation. From two recent donor lung gene expression studies, we reanalysed and paired gene profiles with autoantibody profiles. Primary graft dysfunction can be distinguished by a profile of differentially reactive autoantibodies binding to 17 proteins. Functional analysis showed that 12 of these proteins are part of a protein-protein interaction network (P=3 x 10⁻⁶) involved in proliferative processes. A nearest centroid classifier assigned correct PGD grades to eight out of the nine patients in the validation cohort (P=0·048). We observed significant positive correlation (r=0·63, P=0·011) between differences in IgM reactivity and differences in gene expression levels. This connection between donor lung gene expression and long-lasting recipient IgM autoantibodies towards a specific set of proteins suggests a mechanism for the development of autoimmunity in PGD.
Translating potential biomarker candidates for schizophrenia and depression to animal models of psychiatric disorders (2011)

Schizophrenia and major depressive disorder are severe mental illnesses, which are diagnosed based on patient interviews. Despite many years of extensive research, scientists have not yet fully deciphered how genetic and environmental factors interact to cause these illnesses. Biomarker tests that can confirm diagnoses of schizophrenia or depression are only now beginning to emerge, and could result in a paradigm shift in this field. These tests will help to evaluate the validity of animal models of psychiatric disorders, which are currently characterized based on behavioral measures. In this article, we explore the utility of translating both behavioral and molecular phenotypes of such models to the corresponding human disorders. This approach may help to provide construct validity to animal models and could lead to the identification of models corresponding to defined subtypes of neuropsychiatric disorders based on molecular profiles. Here, we review the molecular and biological pathway alterations that have been found in animal models of schizophrenia and depression and focus on those that are mirrored by similar abnormalities in human patients. Such parallels may provide insight into the validity of specific animal models and therefore help to provide more valuable and accurate tools for the discovery and development of improved psychiatric medications.
Localization of cytochromes to the outer membrane of anaerobically grown Shewanella putrefaciens MR-1 (1992)

In gram-negative bacteria, numerous cell functions, including respiration-linked electron transport, have been ascribed to the cytoplasmic membrane. Gram-negative bacteria which use solid substrates (e.g., oxidized manganese or iron) as terminal electron acceptors for anaerobic respiration are presented with a unique problem: they must somehow establish an electron transport link across the outer membrane between large particulate metal oxides and the electron transport chain in the cytoplasmic membrane. When the metal-reducing bacterium Shewanella putrefaciens MR-1 is grown under anaerobic conditions and membrane fractions are purified from cells lysed by an EDTA-lysozyme-polyoxyethylene cetyl ether (Brij 58) protocol, approximately 80% of its membrane-bound cytochromes are localized in its outer membrane. These outer membrane cytochromes could not be dislodged by treatment with chaotropic agents or by increased concentrations of the nonionic detergent Brij 58, suggesting that they are integral membrane proteins. Cytochrome distribution in cells lysed by a French press protocol confirm the localization of cytochromes to the outer membrane of anaerobically grown cells. This novel cytochrome distribution could play a key role in the anaerobic respiratory capabilities of this bacterium, especially in its ability to mediate manganese and iron reduction.
Antigens: Lipids (2001)

Abstract Phospholipids and glycolipids are major components of biomembranes. Immune responses against them are implicated in several human diseases and in recognition by higher organisms of microbial infections. Structural analysis of lipid antigens is important for understanding the mechanisms of molecular interactions and the pathogenesis of immune abnormalities.
Evaluation of Blood Agar Microtiter Plates for Culturing <i>Leishmania</i> Parasites To Titrate Parasite Burden in Spleen and Peripheral Blood of Patients with Visceral Leishmaniasis (2010)

Serial dilution of blood and spleen biopsy specimens, plated on Novy-MacNeal-Nicolle (NNN) blood agar using microtiter culture plates, is a sensitive and reproducible method for detection and growth of Leishmania parasites. Plates could be easily monitored, and growth could be rapidly detected. Moreover, parasite number may be estimated using this technique.
Quantum Recommendation Systems (2016)

A recommendation system uses the past purchases or ratings of $n$ products by a group of $m$ users, in order to provide personalized recommendations to individual users. The information is modeled as an $m \times n$ preference matrix which is assumed to have a good rank-$k$ approximation, for a small constant $k$. In this work, we present a quantum algorithm for recommendation systems that has running time $O(\text{poly}(k)\text{polylog}(mn))$. All known classical algorithms for recommendation systems that work through reconstructing an approximation of the preference matrix run in time polynomial in the matrix dimension. Our algorithm provides good recommendations by sampling efficiently from an approximation of the preference matrix, without reconstructing the entire matrix. For this, we design an efficient quantum procedure to project a given vector onto the row space of a given matrix. This is the first algorithm for recommendation systems that runs in time polylogarithmic in the dimensions of the matrix and provides an example of a quantum machine learning algorithm for a real world application.
Designing for chaos: applications of chaotic advection at the microscale (2004)

Chaotic advection can play an important role in efficient microfluidic mixers. We discuss a design paradigm that exploits chaotic advection and illustrate by two recent examples, namely enhancing gene expression profiling and constructing an in-line microfluidic mixing channel, how application of this paradigm has led to successful micromixers. We suggest that 'designing for chaos', that is, basing practical mixer design on chaotic advection analysis, is a promising approach to adopt in this developing field which otherwise has little to guide it and is constrained by issues of scale and manufacturability.
Advanced Driver Assistance Systems - Past, present and future (2011)

Every year, automobile manufactures spend millions in funding development of cutting edge technologies to keep drivers safe and accident free while operating their vehicles. These technologies are known in the industry as Advanced Driver Assistance Systems and each one is controlled by complex real-time embedded systems. This paper will present the state of the art for Advanced Driver Assistance Systems and will give detailed overviews of past, present and future designs of each variant. Each overview will focus on the design of the actual real-time embedded system involved.
Development of Novel Simian Immunodeficiency Virus Vectors Carrying a Dual Gene Expression System (2000)

The development of highly efficient and safe gene transfer methods suitable for clinical use is required for human gene therapies. We have developed a novel lentiviral vector system, based on the nonpathogenic simian immunodeficiency virus from African green monkeys (SIVagm), that carries a unique dual gene expression system. This system utilizes the lentivirus Rev responsive element (RRE). Self-inactivating vectors were also developed by deleting a U3 region in the 3' long terminal repeat (3' LTR) of the virus. When pseudotyped with a vesicular stomatitis virus envelope glycoprotein G (VSV-G), the SIVagm-based vectors could transduce both growth-arrested human cells and terminally differentiated neuronal cell lines. Using these vectors, two reporter genes could be expressed simultaneously at equal levels, and expression levels of both genes could be altered by modifying the length of the RRE sequence. These SIVagm-based vectors might offer safety advantages over other lentivirus-based vectors. Furthermore, the novel dual gene expression system described here could increase the usefulness and value of both viral and nonviral vectors in gene therapy.
Guidelines for Dewatering/Densifying Confined Dredged Material. (1978)

Primary emphasis of Task 5A research was oriented toward dewatering fine-grained dredged material resulting from maintenance operations and placed in confined disposal areas. Based on results of research, as synthesized herein, it was determined that: (a) Use of progressive surface trenching concepts to remove disposal area ponded surface water and precipitation and enhance evaporative dewatering of fine-grained dredged material is the most cost-effective dewatering alternative. (b) When existing constraints make it impossible to implement a surface trenching dewatering program, a surface trenching program alone will not produce dewatering at necessary rates, or it is desired to obtain maximum possible dewatering effects, various concepts of either gravity- or vacuum-assisted under-drainage may be applied. (c) Implementation of any program of fine-grained dredged material dewatering and densification will be conducted most effectively as part of an overall confined disposal area management plan. The main technical unknown in application of concepts synthesized in the report is the exact rate at which dewatering will occur. State-of-the-art prediction methods given and referenced in the report are satisfactory for feasibility determinations, and, in many instances, use in final design.
Relative Clinical Usefulness of Glycosylated Serum Albumin and Fructosamine During Short-Term Changes In Glycemic Control in IDDM (1989)

Serial changes in glycosylated blood proteins and direct measures of glycemia were studied in 100 subjects with insulin-dependent diabetes mellitus (IDDM) over a 6-wk period while attempts were made to improve glycemic control. All measures of glycemic control improved significantly (P less than .001). Mean +/- SE glycosylated hemoglobin (HbA1) fell from 9.1 +/- 0.2 to 8.0 +/- 0.1%, glycosylated serum albumin (GSA) from 9.8 +/- 0.4 to 7.3 +/- 0.3%, and fructosamine from 3.92 +/- 0.08 to 3.42 +/- 0.07 mM. Fasting blood glucose levels fell from 11.1 +/- 0.6 to 8.1 +/- 0.7 mM mean blood glucose levels from 12.5 +/- 0.3 to 8.8 +/- 0.03 mM, and the M value from 118 +/- 7 to 40 +/- 3 U. Mean percentage changes in direct measures of glycemia (32-66%) and GSA (29%) were greater than for fructosamine (11%) or HbA, (12%) levels (P less than .001). Furthermore, the correlation between the change in GSA and changes in direct measures of glycemia over the initial 2-wk period was significantly different from the corresponding correlations between direct measures of glycemia and fructosamine over this period (P less than .05-.01). Changes in GSA also correlated more closely than HbA1 or fructosamine did with direct measures of glycemia after 4 and 6 wk. The Spearman rank-correlation coefficient (rs) of absolute changes in GSA, fructosamine, and HbA1 after 2-6 wk ranged from 0.27 to 0.57, confirming that the three measures responded differently to changing glycemic control.(ABSTRACT TRUNCATED AT 250 WORDS)
Complete nucleotide sequence of an infectious clone of human T-cell leukemia virus type II: an open reading frame for the protease gene. (1985)

The entire nucleotide sequence of an infectious clone of human T-cell leukemia virus type II provirus was determined. This provirus consists of 8952 nucleotides. In addition to long terminal repeats and gag, pol, env, and X, a protease gene that is responsible for processing the gag precursor protein was found. The protease gene is encoded in a different frame from gag and pol and was located between the gag and pol open reading frames. The 5' region of the protease gene overlaps the 3' gag region. Coding regions of the provirus show about 60% homology with those of human T-cell leukemia virus type I at the nucleotide level. The evolutionary relationship between human T-cell leukemia virus types I and II is discussed.
ChemInform Abstract: Fluorinated Benzaldehydes in the Reactions of Leuckart and Rodionov. (1990)

Abstract Benzylamines are known to act as inhibitors of N‐methyltransferase.
Neural blockade anesthesia monitor (2004)

ability to monitor the effectiveness of an anesthetic is an area that has not kept pace with the rest of medical technology. Using traditional systems engineering methods, a prototype monitor for local anesthetics was successfully designed and validated. This article describes the clinical physiology of local anesthetics, the selection of technologies to measure the physiological responses, the monitor design process, and the results of clinical trials. The subject neural blockade monitor provides a noninvasive, real-time tool for the anesthesiologist. Synergistic blending of systems engineering and biomedical engineering resulted in a highly effective prototype that was developed in a relatively short period of time.
PLL-Based Battery Charge Circuit Topology (2004)

In this paper, a phase-locked battery charger (PLBC) is proposed to show that a phase-locked loop (PLL) is a perfect circuit topology for battery charging. The circuit topology of the PLBC is almost the same as that of the PLL and it inherits the merits of the PLL, such as autotracking, autolocking, and high accuracy. A complete charging process, consisting of three subprocesses: constant current charge, variable current charge, and float charge, can be automatically implemented by using the above inherent characteristics of the PLL. Experimental results show that the PLL is really suitable for carrying out a battery charge controller.
Effector CD4 and CD8 T Cells and Their Role in the Tumor Microenvironment (2012)

T cells in tumors-the so-called tumor infiltrating lymphocytes (TIL) have been studied intensively over the past years. Compelling evidence point to a clinical relevance for high numbers of T cells at the tumor site with CD8 memory T cells as a key denominator for overall survival (OS) in patients with colo-rectal cancer (CRC), and also for others solid cancers. These data goes hand in hand with studies of clonality of TIL showing the T cells among TIL are expanded clonally, and also that tumor specific T cells of CD4 as well as CD8 type are enriched at the tumor site. The tumor microenvironment is hostile to T cell function e.g., due to expression of enzymes that depletes the amino acids tryptophan and arginine, high concentration of tumor secreted lactate, and presence innate cells or regulatory T cells both with suppressive activity. Analyses of the specificity of TILs in melanoma demonstrate that quite few known antigens are in fact recognized by these cultures underscoring patient unique and/or mutated antigens may represent important target for recognition.
Malondialdehyde tagging improves the analysis of arginine oligomers and arginine‐containing dendrimers by HPLC‐MS (2008)

The selective modification of arginine residues by malondialdehyde (MDA) was used to improve the mass spectrometric analysis of arginine oligomers (Arg(x), x = 4, 6, 7, 8, 9) and an arginine-containing dendrimeric peptide. MDA tagging significantly increased the hydrophobicity of the arginine side-chain and resulted in improved retention in RP HPLC of the oligoarginines using formic acid as mobile phase additive. This avoided the use of TFA to generate sufficient retention, as TFA was shown to lead to a dramatically reduced sensitivity (up to ten-fold for Arg(8) and Arg(9)) as a result of the strong signal suppression by ion pairing with multiple basic residues. MDA modification of Arg oligomers not only resulted in improved detection sensitivity for most of the peptides studied (e. g., more than six-fold for Arg(7)), but also greatly enhanced the quality of MS/MS spectra, in line with previous results for other peptides. Furthermore, MDA modification helped to identify major side products in a sample of a dendrimeric peptide, a class of peptides that is typically difficult to analyze by MS.
Dynamics of neuronal firing correlation: modulation of "effective connectivity" (1989)

1. We reexamine the possibilities for analyzing and interpreting the time course of correlation in spike trains simultaneously and separably recorded from two neurons. 2. We develop procedures to quantify and properly normalize the classical joint peristimulus time scatter diagram. These allow separation of the "raw" correlation into components caused by direct stimulus modulations of the single-neuron firing rates and those caused by various types of interaction between the two neurons. 3. A newly developed significance test ("surprise") is applied to evaluate such inferences. 4. Application of the new procedures to simulated spike trains allowed the recovery of the known circuitry. In particular, it proved possible to recover fast stimulus-locked modulations of "effective connectivity," even if they were masked by strong direct stimulus modulations of individual firing rates. These procedures thus present a clearly superior alternative to the commonly used "shift predictor." 5. Adopting a model-based approach, we generalize the classical measures for quantifying a direct interneuronal connection ("efficacy" and "contribution") to include possible stimulus-locked time variations. 6. Application of the new procedures to real spike trains from several different preparations showed that fast stimulus-locked modulations of "effective connectivity" also occur for real neurons.
A Voxel-Based Method for Automated Identification and Morphological Parameters Estimation of Individual Street Trees from Mobile Laser Scanning Data (2013)

As an important component of urban vegetation, street trees play an important role in maintenance of environmental quality, aesthetic beauty of urban landscape, and social service for inhabitants. Acquiring accurate and up-to-date inventory information for street trees is required for urban horticultural planning, and municipal urban forest management. This paper presents a new Voxel-based Marked Neighborhood Searching (VMNS) method for efficiently identifying street trees and deriving their morphological parameters from Mobile Laser Scanning (MLS) point cloud data. The VMNS method consists of six technical components: voxelization, calculating values of voxels, searching and marking neighborhoods, extracting potential trees, deriving morphological parameters, and eliminating pole-like objects other than trees. The method is validated and evaluated through two case studies. The evaluation results show that the completeness and correctness of our method for street tree detection are over 98%. The derived morphological parameters, including tree height, crown diameter, diameter at breast height (DBH), and crown base height (CBH), are in a good agreement with the field measurements. Our method provides an effective tool for extracting various morphological parameters for individual street trees from MLS point cloud data.
Immunosuppressive activity of lymphocyte mitogenesis by breast cancer-associated p43. (1996)

Placental isoferritin (PLF), an acidic isoform of ferritin, and its unique superheavy chain of 43 kDa (p43) has been described to be synthesized by human breast cancer cells. Physiologically, p43 PLF produced by the placenta is involved in immune suppression of maternal lymphocytes aimed at fetal antigens. A study was carried out to elucidate a paradigm of p43 occurrence in breast cancer patients. Immunosuppression of cytotoxic CD8+ lymphocytes was measured via inhibition of blast transformation in concanavalin A (ConA) stimulated peripheral blood lymphocytes (PBL) using 3H-thymidine uptake in vitro. PBLs were cultivated from 29 women having benign lesions in the breast as well as from 41 patients with breast adenocarcinoma. In breast cancer patients addition of p43 significantly inhibited the activation of lymphocytes proliferation by ConA compared to women with benign tumors. The addition of indomethacin or levamisole did not influence this inhibitory effect of p43 in breast cancer patients. Presence of interleukin-2 in cultures was able to overcome the inhibitory effect of p43 on CD8+ lymphocytes proliferation from women having breast adenocarcinomas and to increase its value in patients with benign lesions.
Experience with joint AGC regulation (1994)

Operating generators on automatic generation control (AGC) to follow load fluctuations has often been considered an unavoidable cost of doing business. However, several months of testing and more than two years of commercial operation have demonstrated that there can be significant benefits in transferring AGC regulation from three predominantly thermal-based utilities to a fourth predominantly hydro-based utility. This arrangement called joint AGC regulation successfully transfers high frequency regulation components for reduced fuel and maintenance costs and allows dynamic interchange scheduling to achieve flexible generation scheduling and improved economic dispatch. Successful implementation involved development of a joint AGC regulation control strategy and an evaluation of the tangible and intangible costs of providing AGC regulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High-power and wide wavelength range GaN-based laser diodes (2006)

Since the first demonstration of a pulsed InGaN laser diodes (LDs) grown on sapphire substrate in 1995, we have been developing longer lifetime and higher optical output power LDs in the 400 - 410 nm wavelength range. Moreover, we have already succeeded in the expansion of the lasing wavelength range from ultraviolet (UV) to blue-green. In this paper, we reported the recent progress of high-power and wide wavelength range GaN-based LDs with an optical output power of 20 mW single mode (375nm), 160 mW single mode (405nm), 200 mW multi mode (405nm), 50 mW single mode (445nm), 300 mW multi mode (445nm), and 20 mW single mode (473nm).
Evidence of a Strained Pore Wall Structure in Mesoporous Silica FSM-16 Studied by X-ray Absorption Spectroscopy (2007)

The local structure around Si species in mesoporous silica FSM-16 was investigated by Si K-edge XAFS. As expected from the previous studies, the local symmetry of Si species in FSM-16 is almost identical to that of amorphous silica. The Si−O bond length was longer than those of α-quartz, ZSM-5, and amorphous silica. Relations between the prolonged bond length and the acidic property of FSM-16 were discussed.