gebhart/patrepeval huggingface dataset:
High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories (2010)

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.
Prevalence of hyperhomocyst(e)inemia in patients with peripheral arterial occlusive disease. (1989)

A micromethod adapted for automated determinations was used to measure basal plasma levels of homocyst(e)ine [H(e)]. These levels included the sum of free and bound forms of homocysteine, its disulfide oxidation product, homocystine, and the homocysteine-cysteine-mixed disulfide. Two groups of subjects were studied: apparently healthy individuals (n = 103) and patients with peripheral arterial occlusive disease (PAOD) (n = 47). Because age in PAOD patients was higher than in control subjects, the control subjects were subdivided into younger and older groups (aged 60 years or less and more than 60 years, respectively). The H(e) levels in the younger groups were 11.18 +/- 3.58 (mean +/- SD, expressed as homocysteine) and 8.58 +/- 2.82 nmol/ml in men and women, respectively; in the older groups, the levels were 10.74 +/- 2.16 and 9.04 +/- 2.16 nmol/ml in men and women, respectively. There was a positive correlation of H(e) levels with age in the younger control women (r = 0.373; p less than 0.02); no significant correlations were present in the other three control groups. Levels of H(e) in PAOD patients (15.44 +/- 5.76 and 17.04 +/- 8.26 nmol/ml in men and women, respectively) were significantly higher than those indicated above in the older controls. Next, the PAOD patients were assigned to two subgroups: 1) those with normal levels of H(e) (within two standard deviations of the mean of the control values) and 2) those with elevated levels of H(e). Age, cholesterolemia, and the prevalence of smoking and diabetes were similar in both subgroups. These results suggest that elevated plasma H(e) is an independent risk factor for arterial occlusive disease.
Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in <i>Arabidopsis thaliana</i> (2001)

The intranuclear arrangements of centromeres and telomeres during meiotic interphase and early prophase I of meiosis in Arabidopsis thaliana were analysed by fluorescent in situ hybridisation to spread pollen mother cells and embryo-sac mother cells. Meiocyte identification, staging and progression were established by spreading and sectioning techniques, including various staining procedures and bromodeoxyuridine labeling of replicating DNA. Centromere regions of Arabidopsis are unpaired, widely dispersed and peripherally located in nuclei during meiotic interphase, and they remain unpaired and unassociated throughout leptotene. Eventually they associate pairwise during zygotene, as part of the nucleus-wide synapsis of homologous chromosomes. Telomeres, by contrast, show a persistent association with the nucleolus throughout meiotic interphase. Variation in telomere signal number indicates that telomeres undergo pairing during this interval, preceding the onset of general chromosome synapsis. During leptotene the paired telomeres lose their association with the nucleolus and become widely dispersed. As the chromosomes synapse during zygotene, the telomeres reveal a loose clustering within one hemisphere, which may represent a degenerate or relic bouquet configuration. We propose that in Arabidopsis the classical leptotene/zygotene bouquet is absent and is replaced functionally by nucleolus-associated telomere clustering.
Alemtuzumab (Millennium/ILEX). (2001)

Alemtuzumab, a lymphocyte-depleting humanized monoclonal antibody, is being developed by Millennium Pharmaceuticals Inc and ILEX Oncology for the potential treatment of chronic lymphocytic leukemia (CLL) [274580]. The utility of the compound for treating bone marrow (BM) stem cell transplantation-associated graft-versus-host disease (GVHD) [372946] and for ex vivo purging of BM to remove malignant T-cells [244056] is also being investigated. Additional potential therapeutic areas for which clinical trials are planned or ongoing include vasculitis, multiple sclerosis [288762] and organ transplantation [338304]. A Biologics License Application (BLA) was filed with the FDA in December 1999 by ILEX and Millennium [351523], [351524], [373873]. The FDA accepted the application for filing in February 2000 [355775] and returned a complete response letter in June 2000 [372172]. Millennium and ILEX submitted a response to the FDA in August 2000 [379766]. Alemtuzumab has received Fast Track designation [304771] and orphan drug status from the FDA [288762], and the drug was reviewed by the FDA's Oncologic Drugs Advisory Committee on 14 December, 2000 [387228]. The committee voted 14 to 1 to recommend accelerated approval of alemtuzumab for patients with CLL who have been treated with alkylating agents and who have failed fludarabine therapy [393778], [393894]. In March 2000, Millennium and ILEX also submitted a Marketing Authorization Application (MAA) for alemtuzumab to the European Agency for the Evaluation of Medicinal Products (EMEA) [363595]. In October 2000, EMEA accepted the MAA for alemtuzumab under the agency's centralized approval procedure [387228]. Alemtuzumab was originally synthesized by Herman Waldmann and colleagues at Cambridge University and licensed to Burroughs Wellcome (BW) via the British Technology Group (BTG) [162622]. BW conducted phase I and II trials for a broad range of indications, but then discontinued development because of disappointing results in phase II rheumatoid arthritis trials [326848]. In April 1997, LeukoSite licensed rights to the antibody from BTG for the treatment of CLL and prolymphocytic leukemia, plus an option to develop it for other indications. BW agreed to supply LeukoSite with intellectual property [244056], [326848]. In May 1997, LeukoSite entered into a joint venture with ILEX Oncology for the further development of alemtuzumab [245986]. By the end of 1999, Millennium acquired LeukoSite with commitment to pursue development of the compound through the joint venture Millennium & ILEX Partners LP [351523], [370237]. In August 1999, Schering AG and its US affiliate Berlex Laboratories obtained exclusive worldwide marketing rights for alemtuzumab, excluding Japan and East Asia. In the US, Berlex, Millennium and ILEX will divide profits from alemtuzumab sales equally [337702], [338837].
Systematic review and meta-analysis of survival following extracorporeal liver support (2011)

ELS systems appear to improve survival in acute liver failure. There is, however, no evidence that they improve survival in acute-on-chronic liver failure.
Sound absorption by subwavelength membrane structures: A geometric perspective (2015)

Decorated membranes comprising a thin layer of elastic film with small rigid platelets fixed on top have been found to be efficient absorbers of low-frequency sound. In this work we consider the problem of sound absorption from a perspective aimed at deriving upper bounds under different scenarios, i.e., whether the sound is incident from one side only or from both sides, and whether there is a reflecting surface on the back side of the membrane. By considering the negligible thickness of the membrane, usually on the order of a fraction of one millimeter, we derive a relation showing that the sum of the incoming sound waves' (complex) pressure amplitudes, averaged over the area of the membrane, must be equal to that of the outgoing waves. By using this relation, and without going to any details of the wave solutions, it is shown that the maximum absorption achievable from one-sided incidence is 50%, while the maximum absorption with a back-reflecting surface can reach 100%. The latter was attained by the hybridized resonances. All the results are shown to be in excellent agreement with the experiments. This generalized perspective, when used together with the Green function's formalism, can be useful in gaining insights into the constraints on what are achievable in scatterings and absorption by thin film structures and delineating them.
SDN-Based Virtual Machine Management for Cloud Data Centers (2016)

Software-defined networking (SDN) is an emerging paradigm to logically centralize the network control plane and automate the configuration of individual network elements. At the same time, in cloud data centers (DCs), although network and server resources are collocated and managed by a single administrative entity, disjoint control mechanisms are used for their respective management. In this paper, we propose a unified server-network resource management for such converged information and communication technology (ICT) environments. We present a SDN-based orchestration framework for live virtual machine (VM) management that exploits temporal network information to migrate VMs and minimize the network-wide communication cost of the resulting traffic dynamics. A prototype implementation is presented, and a cloud DC testbed is used to evaluate the impact of diverse orchestration algorithms. Our live VM management has been shown to reduce the network-wide communication cost, especially for the high-cost and congestion-prone core and aggregation layers of the DC. Our results show an increase in network-wide throughput by over six times, as well as over 70% communication cost reduction by migrating less than 50% of the VMs.
[Demonstration of enkephalins in pheochromocytoma]. (1982)

Adrenal medulla has recently been shown to contain high concentrations of enkephalin immunoreactive peptides. In the present study, we report the levels of M-ENK and L-ENK in extracts from 6 cases of human pheochromocytoma. The molecular forms of M-ENK have been characterized by gel filtration chromatography and HPLC. mRNA extracted from one tumor has been proved to code for a 80,000 kilo daltons protein containing M-ENK sequence. M-ENK immunoreactive peptides are secreted in the culture medium of dispersed cultured cells of human pheochromocytoma. This secretion is stimulated when nicotine (10(5) M) is added to the medium. However, the level of plasma M-ENK in pheochromocytoma patients is not significantly different from normal patients. Data from Holaday and al. have established that naloxone (an opiate antagonist) has a beneficial role in shock. But the origin and meaning of plasma M-ENK remain to be established.
Respect my authority! (2006)

We present an approach to improving the precision of an initial document ranking wherein we utilize cluster information within a graph-based framework. The main idea is to perform reranking based on centrality within bipartite graphs of documents (on one side) and clusters (on the other side), on the premise that these are mutually reinforcing entities. Links between entities are created via consideration of language models induced from them.We find that our cluster-document graphs give rise to much better retrieval performance than previously proposed document-only graphs do. For example, authority-based reranking of documents via a HITS-style cluster-based approach outperforms a previously-proposed PageRank-inspired algorithm applied to solely-document graphs. Moreover, we also show that computing authority scores for clusters constitutes an effective method for identifying clusters containing a large percentage of relevant documents.
Depression and Psychosomatic Illness (1974)

Current concepts of depression recognize that it may have many roots including genetic, constitutional, biochemical, neurophysiological, sociocultural and psychodynamic factors. Depression can be overt and quite evident; yet in many instances it can be masked, hidden by more noticeable somatic symptoms and even somatic disease. Concepts of psychosomatic illness have undergone considerable change in that the ‘specificity’ theories which prevailed 30 years ago have been superseded by the current belief that all illness is psychosomatic and not limited to a few chosen ones. Depression is often intertwined and interwoven with psychosomatic illness since it can be the trigger that precipitates a somatic illness. It can also be the result.
Classification of non-speech human sounds: Feature selection and snoring sound analysis (2009)

Human sounds can be roughly divided into two categories: speech and non-speech. Traditional audio scene analysis research puts more emphasis on the classification of audio signals into human speech, music, and environmental sounds. We take a different perspective in this paper. We are mainly interested in the analysis of non-speech human sounds, including laugh, screaming, sneeze, and snore. Toward this goal, we investigate many commonly used acoustic features and select useful ones for classification using multivariate adaptive regression splines (MARS) and support vector machine (SVM). To evaluate the robustness of the selected features, we also perform extensive simulations to observe the effect of noise on the accuracy of the classification. Finally, for the class of snoring sounds, we propose a robust approach to further categorize them into simple snores and snores of subjects with obstructive sleep apnea (OSA).
Comprehensive Compositional Analysis of Plant Cell Walls (Lignocellulosic biomass) Part I: Lignin (2010)

The need for renewable, carbon neutral, and sustainable raw materials for industry and society has become one of the most pressing issues for the 21st century. This has rekindled interest in the use of plant products as industrial raw materials for the production of liquid fuels for transportation(1) and other products such as biocomposite materials(7). Plant biomass remains one of the greatest untapped reserves on the planet(4). It is mostly comprised of cell walls that are composed of energy rich polymers including cellulose, various hemicelluloses (matrix polysaccharides, and the polyphenol lignin(6) and thus sometimes termed lignocellulosics. However, plant cell walls have evolved to be recalcitrant to degradation as walls provide tensile strength to cells and the entire plants, ward off pathogens, and allow water to be transported throughout the plant; in the case of trees up to more the 100 m above ground level. Due to the various functions of walls, there is an immense structural diversity within the walls of different plant species and cell types within a single plant(4). Hence, depending of what crop species, crop variety, or plant tissue is used for a biorefinery, the processing steps for depolymerization by chemical/enzymatic processes and subsequent fermentation of the various sugars to liquid biofuels need to be adjusted and optimized. This fact underpins the need for a thorough characterization of plant biomass feedstocks. Here we describe a comprehensive analytical methodology that enables the determination of the composition of lignocellulosics and is amenable to a medium to high-throughput analysis. In this first part we focus on the analysis of the polyphenol lignin (Figure 1). The method starts of with preparing destarched cell wall material. The resulting lignocellulosics are then split up to determine its lignin content by acetylbromide solubilization(3), and its lignin composition in terms of its syringyl, guaiacyl- and p-hydroxyphenyl units(5). The protocol for analyzing the carbohydrates in lignocellulosic biomass including cellulose content and matrix polysaccharide composition is discussed in Part II(2).
Efficient Dc-free RLL codes for optical recording (2002)

We report on new runlength-limited codes (RLL) intended for the next generation of DVD. The efficiency of the newly developed RLL schemes is extremely close to the theoretical maximum, and as a result, significant density gains can be obtained with respect to prior art coding methods.
A Face and Palmprint Recognition Approach Based on Discriminant DCT Feature Extraction (2004)

In the field of image processing and recognition, discrete cosine transform (DCT) and linear discrimination are two widely used techniques. Based on them, we present a new face and palmprint recognition approach in this paper. It first uses a two-dimensional separability judgment to select the DCT frequency bands with favorable linear separability. Then from the selected bands, it extracts the linear discriminative features by an improved Fisherface method and performs the classification by the nearest neighbor classifier. We detailedly analyze theoretical advantages of our approach in feature extraction. The experiments on face databases and palmprint database demonstrate that compared to the state-of-the-art linear discrimination methods, our approach obtains better classification performance. It can significantly improve the recognition rates for face and palmprint data and effectively reduce the dimension of feature space.
Biochemical Characterization of Recombinant Fusions of Lipopolysaccharide Binding Protein and Bactericidal/Permeability-increasing Protein (1997)

The physiological response to endotoxin (lipopolysaccharide (LPS)) can be regulated by two closely related LPS-binding proteins, LPS-binding protein (LBP), which potentiates LPS' inflammatory activity via interaction with the monocytic antigen CD14, and bactericidal/permeability-increasing protein (BPI), which neutralizes LPS. Both proteins bind LPS with high affinity sites in their N-terminal domains, whereas interaction between LBP and CD14 is dependent upon the LBP C-terminal domain. We have created fusions of the N- and C-terminal domains from each protein and compared the functional activities and pharmacokinetics of these fusions, the individual N-terminal domains, and the parent proteins. The N-terminal domains of BPI and LBP bound lipid A with their characteristic apparent affinity constants, regardless of the C-terminal fusion partner. In addition, the C-terminal domain of LBP allowed transfer of LPS to CD14 in conjunction with either N-terminal LPS binding domain. Proteins containing a BPI N-terminal domain had greater heparin binding capacities in vitro and were cleared more rapidly from the plasma of whole animals. Taken together, these data better define how closely related proteins such as BPI and LBP can have opposing effects on the body's response to LPS.
Evolutionary Anthropology Society (2007)

•20 Years of Biocultural Research in Dominica: The Bwa Mawego Child Stress ProjectMark Flinn, Robert Quinlan, David Leone
Early Detection of Alzheimer’s Disease with PET Imaging (2010)

Preclinical diagnosis of Alzheimer's disease (AD) is one of the major challenges for the prevention of AD. AD biomarkers are needed not only to reveal preclinical pathologic changes, but also to monitor progression and therapeutics. PET neuroimaging can reliably assess aspects of the molecular biology and neuropathology of AD. The aim of this article is to review the use of FDG-PET and amyloid PET imaging in the early detection of AD.
Myelin under stress (2009)

The capacity to fold proteins properly is fundamental for cell survival. Secreted and transmembrane proteins are synthesized in the endoplasmic reticulum (ER), an organelle that has the ability to discriminate between native and nonnative proteins, in a process called protein quality control. When folding is not properly achieved, misfolded proteins can accumulate. The terminally misfolded proteins are typically retrotranslocated into the cytoplasm for degradation by the proteasome, in a process known as endoplasmic reticulum-associated degradation. However, if the degradation is insufficient, accumulation of abnormal proteins in the ER activates the unfolded protein response (UPR), a complex set of new signals aimed to reduce further the load of abnormal protein in the ER. Massive synthesis of myelin lipids and proteins is necessary to support myelinogenesis. Not surprisingly, therefore, ER stress (including the UPR), the proteasome, and autophagy (lysosomes) have been implicated in myelin disorders, such as Pelizaeus-Merzbacher disease and vanishing white matter disease in the central nervous system and Charcot-Marie-Tooth neuropathies in the peripheral nervous system. Here we discuss recent evidence supporting an important role for ER stress in myelin disorders.
High-performance single-chip exon capture allows accurate whole exome sequencing using the Illumina Genome Analyzer (2011)

Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform. The protocol involves two-stage library construction. The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold. Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants. Our protocol is also well suited for use with whole genome amplified DNA. The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.
Enhancement of hippocampal LTP, reference memory and sensorimotor gating in mutant mice lacking a telencephalon‐specific cell adhesion molecule (2001)

Telencephalin (TLCN) is a cell adhesion molecule selectively expressed in the telencephalon of the mammalian brain. The mutant mice lacking TLCN had no detectable abnormalities in their neural development and synaptic structures. Ablation of TLCN increased the hippocampal long-term potentiation and its saturation level. The TLCN mutation selectively enhanced the performance of the radial maze and water-finding tasks, learning tasks with appetitive reinforcers, but not the contextual fear conditioning and Morris water maze tasks with aversive stimuli for conditioning. Furthermore, the TLCN mutant mice showed an increase of prepulse inhibition of the acoustic startle response. These results suggest that TLCN is a determinant of the dynamic range of synaptic plasticity and plays roles in reward-motivated learning and memory and sensorimotor gating.