gebhart/patrepeval huggingface dataset:
In-vitro susceptibility of Aspergillus spp. isolates to amphotericin B and itraconazole (1999)

The MICs of amphotericin B and itraconazole for 230 isolates of Aspergillus spp., comprising 156 Aspergillus fumigatus, 20 Aspergillus terreus, 22 Aspergillus flavus, 17 Aspergillus nidulans and 15 Aspergillus niger, were determined by a broth microdilution method with RPMI 1640 medium. No isolate was detected with an MIC of amphotericin B >2 mg/L. Itraconazole MICs >16 mg/L were detected for four Aspergillus fumigatus and one Aspergillus nidulans isolates.
Health issues of whey proteins: 1. Protection of lean body mass (2006)

Loss of muscle mass as a consequence of changes in protein metabolism during periods of catabolic stress is a serious complication in a variety of conditions. These conditions are weight loss programs, sarcopenia in the elderly and several clinical states. It appears from many studies that improved protein nutrition by ingestion of high-quality proteins can help to decrease loss of lean body mass. Essential amino acids, especially branched-chain amino acids (BCAA) and cysteine are implicated as key factors in this regard. Since whey protein is one of the best naturally occurring proteins in terms of digestibility and concentration of BCAA and cysteine, this paper reviews the significance of whey protein for protection of lean body mass. It is concluded that whey proteins will help to reduce unwanted loss of muscle mass during weight loss regimens. Ingestion of whey will contribute to an increase of muscle mass during exercise programs, designed to prevent or reduce sarcopenia in the very old. Moreover, ingestion of whey protein is useful in the prevention of muscle mass loss in (clinical) catabolic conditions. The extent to which whey protein offers a specific nutritional advantage in humans over other high-quality proteins needs to be assessed. Copyright Â© 2006 by New Century Health Publishers, LLC.
Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model (2002)

When conditions cause bacterial growth to stop, extensive reprogramming of physiology and gene expression allows for the cell's survival. We used whole-genome DNA arrays to determine the system response in Escherichia coli cells experiencing transient growth arrest caused by glucose-lactose diauxie and H2O2 treatment, and also entry into stationary phase. The results show that growth-arrested cells induce stringent control of several gene systems. The vast majority of genes encoding the transcription and translation apparatus immediately downregulate, followed by a global return to steady state when growth resumes. Approximately one-half of the amino acid biosynthesis genes downregulate during growth arrest, with the notable exception of the his operon, which transiently upregulates in the diauxie experiment. Nucleotide biosynthesis downregulates, a result that is again consistent with the stringent response. Likewise, aerobic metabolism downregulates during growth arrest, and the results led us to suggest a model for stringent control of the ArcA regulon. The stationary phase stress response fully induces during growth arrest, whether transient or permanent, in a manner consistent with known mechanisms related to stringent control. Cells similarly induce the addiction module anti-toxin and toxin genes during growth arrest; the latter are known to inhibit translation and DNA replication. The results indicate that in all aspects of the response cells do not distinguish between transient and potentially permanent growth arrest (stationary phase). We introduce an expanded model for the stringent response that integrates induction of stationary phase survival genes and inhibition of transcription, translation and DNA replication. Central to the model is the reprogramming of transcription by guanosine tetraphosphate (ppGpp), which provides for the cell's rapid response to growth arrest and, by virtue of its brief half-life, the ability to quickly resume growth as changing conditions allow.
Advanced glycation end products induce glomerular sclerosis and albuminuria in normal rats. (1994)

High levels of tissue advanced glycation end products (AGEs) that result from the spontaneous modification of proteins by glucose occur in diabetes and aging. To address the potential pathogenic role of AGEs in the glomerulosclerosis of diabetes or nephrosclerosis of aging, doses of AGE-modified rat albumin (25 mg per kg per day, i.v.) sufficient to elevate circulating AGE levels to the range of diabetic serum were administered daily to healthy rats alone or in combination with the AGE inhibitor aminoguanidine. After 5 months, the AGE content of renal tissues in AGE-treated rats rose to 50% above controls (P < 0.025), whereas serum contained 2.8-fold greater AGE levels (P < 0.025). Light and electron microscopy of kidneys from AGE-treated rats revealed a more than 50% increase in glomerular volume compared to controls (P < 0.001), significant periodic acid/Schiff reagent-positive deposits, basement membrane widening, and mesangial extracellular matrix increase and indicated significant glomerulosclerosis compared to untreated (P < 0.002) or albumin-treated controls (P < 0.002). These changes were associated with significant loss of protein (P < 0.005) and albumin (P < 0.002) in the urine of AGE-treated rats compared to controls. Cotreatment with aminoguanidine markedly limited both the structural and functional defects. These in vivo data demonstrate that AGEs influence glomerular structure and function in a manner leading to glomerulosclerosis. The effects are AGE-specific, as they are ameliorated by a pharmacological AGE inhibitor, aminoguanidine.
The AlCl3–LiAlH4 reduction of Δ9(11)-12-oxo and Δ9(11)-12-hydroxy steroids (1968)

Desoxycholic acid and 3α,12α-dihydroxypregnane were transformed to the corresponding Δ 9(11) -12-oxo compounds. These steroids and their NaBH 4 reduction products were then hydrogenolyzed with AlCl 3 –LiAlH 4 to provide Δ 9(11) -compounds in good yield.
Reversal of colchicine-induced mitotic arrest in Chinese hamster cells with a colchicine-specific monoclonal antibody. (1990)

The ability of a high-affinity colchicine-binding monoclonal antibody to reverse the effects of colchicine on Chinese hamster ovary cells was investigated. Using flow cytometry, a complete mitotic blockade was demonstrated after 16 hours with 2.5 x 10(-7) mol/l (molar) colchicine. Colchicine-induced changes were reversible when equimolar antibody was added simultaneously with or up to 6 hours after colchicine. With further delay in addition of antibody, a progressive irreversible increase in mitotic blockade and increase in mean cell size was observed. Prolonged colchicine exposure, without antibody reversal, led to polyploidy and structural chromosome breakage. Early antibody reversal restored cells to the diploid state, whereas delayed reversal resulted in a time-dependent increase in polyploidy. Colchicine-induced polyploidy and chromosomal aberrations may be the basis for both colchicine toxicity and the time-dependent increase in irreversibility of colchicine effects.
Liquid-Liquid Phase Separation in Biology (2014)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary to understand the consequences of liquid-like states for biological functions.
A New System Architecture for Future Long-Term High-Density Neural Recording (2013)

This brief presents a new system architecture for neural recording to allow higher recording density and more tolerance to interface degeneration and artifacts. Compared with its conventional counterpart, the proposed architecture has a frequency-dependent gain stage that inherently rejects dc offset and attenuates low-frequency interferences. In the digital domain, frequency compensation is used to restore the signals “seen” by an electrode. Powered by a switched-capacitor design, the proposed architecture can lead to major improvements on system performance metrics, including input impedance, distortion, and dynamic range. In simulations with different electrode sizes and degeneration levels, the proposed architecture consistently gives high-fidelity recording data. We argue that the proposed architecture is more suitable for long-term high-density invasive brain-computer interface experiments as a replacement to better support a mimicked “Moore's Law” on recording density.
Microfluidic blood sample preparation for rapid sepsis diagnostics (2012)

Sepsis, commonly referred to as blood poisoning, is a serious medical condition characterized by a whole-body inflammatory state caused by microbial infection. Rapid treatment is crucial, however, traditional culture-based diagnostics usually takes 2-5 days. The overall aim of the thesis is to develop microfluidic based sample preparation strategies, capable of isolating bacteria from whole blood for rapid sepsis diagnostics. Although emerging technologies, such as microfluidics and “lab-on-a-chip” (LOC) devices have the potential to spur the development of protocols and affordable instruments, most often sample preparation is performed manually with procedures that involve handling steps prone to introducing artifacts, require skilled technicians and well-equipped, expensive laboratories. Here, we propose the development of methods for fast and efficient sample preparation that can isolate bacteria from whole blood by using microfluidic techniques with potential to be incorporated in LOC systems. We have developed two means for high throughput bacteria isolation: size based sorting and selective lysis of blood cells. To process the large blood samples needed in sepsis diagnostics, we introduce novel manufacturing techniques that enable scalable parallelization for increased throughput in miniaturized devices. The novel manufacturing technique uses a flexible transfer carrier sheet, water-dissolvable release material, poly(vinyl alcohol), and a controlled polymerization inhibitor to enable highly complex polydimethylsiloxane (PDMS) structures containing thin membranes and 3D fluidic networks. The size based sorting utilizes inertial microfluidics, a novel particles focusing method that operates at extremely high flow rates. Inertial focusing in flow through a single inlet and two outlet, scalable parallel channel devices, was demonstrated with filtration efficiency of &amp;gt;95% and a flowrate of 3.2 mL/min. Finally, we have developed a novel microfluidic based sample preparation strategy to continuously isolate bacteria from whole blood for downstream analysis. The method takes advantage of the fact that bacteria cells have a rigid cell wall protecting the cell, while blood cells are much more susceptible to chemical lysis. Whole blood is continuously mixed with saponin for primary lysis, followed by osmotic shock in water. We obtained complete lysis of all blood cells, while more than 80% of the bacteria were readily recovered for downstream processing. Altogether, we have provided new bacteria isolation methods, and improved the manufacturing techniques and microfluidic components that, combined offer the potential for affordable and effective sample preparation for subsequent pathogen identification, all in an automated LOC format.
The role of the central amygdala in stress and adaption. (1997)

Recent views on stress emphasise the existence of more than one response pattern to stressful events, and the importance of individual differences in coping with environmental challenges. Therefore, in the evaluation of the specific contribution of the central nucleus of the amygdala (CEA) in stress and adaptation it has to be considered whether the stress is acute or conditioned, and whether it requires active or passive styles of coping. Based on series of our own studies, we propose that the CEA is consistently involved in the organisation of processes of passive coping, reflected in immobile behaviour and parasympathetic activity. Furthermore, a differential regulation of the CEA via its peptidergic neuronal input may underlie the distinct behavioural and physiological stress patterns accompanying the different styles of coping. Additionally, the involvement of the CEA in neuroendocrine control is addressed. The CEA exerts a general, modulatory influence on the neuroendocrine control to acute stressors, whereas this output during conditioned stress seems to be independent of the CEA. The neuroendocrine state as achieved during acute stress is, via feedback to the brain, of importance in learning about the situation, and to consolidate the experience. In this review an attempt is made to provide an integrated model of CEA functioning in relation to stress and adaptation.
A microfabricated 3-D stem cell delivery scaffold for retinal regenerative therapy (2009)

Thesis (M. Eng.)--Harvard-MIT Division of Health Sciences and Technology, 2009.
Thrombolytic and Pharmacokinetic Properties of Human Tissue-Type Plasminogen Activator Variants, Obtained by Deletion and/or Duplication of Structural/Functional Domains, in a Hamster Pulmonary Embolism Model (1991)

A pulmonary embolism model in hamsters was used for the quantitative evaluation of the thrombolytic and pharmacokinetic properties of variants of tissue-type plasminogen activator (t-PA). A 25 microliters 125I-fibrin labeled human plasma clot was made in vitro and injected into the jugular vein of heparinized hamsters. The extent of thrombolysis within 90 min was determined as the difference between the radioactivity injected in the jugular vein and that recovered in the heart and lungs. Recombinant t-PA (home-made rt-PA or Activase) infused intravenously over 60 min caused dose-dependent progressive thrombolysis. The results of thrombolytic potency (clot lysis in percent versus dose administered in mg/kg) and of specific thrombolytic activity (clot lysis in percent versus steady state plasma level in microgram/ml) were fitted with an exponentially transformed sigmoidal function y = 100 c/(1 + e-a(ax-eh] and the maximal percent lysis (c), the dose or plasma level at which maximal rate of lysis is achieved (b) and the maximal rate of lysis (z = 1/4 ac.eb) were determined. With rt-PA, these parameters were c = 72 +/- 6% (mean +/- SEM), b = 0.19 +/- 0.08 mg/kg, z = 68 +/- 25% lysis per mg/kg, with corresponding values of 87 +/- 5%, 0.07 +/- 0.03 mg/kg and 150 +/- 38% lysis per mg/kg for Activase (p = NS). Deletion of the finger and growth factor domains in rt-PA (rt-PA-delta FE) was not associated with marked alteration of the thrombolytic potency (c = 90 +/- 30%, b = 0.34 +/- 0.35 mg/kg, and z = 54 +/- 14% per mg/kg), but was associated with a significant reduction of the specific thrombolytic activity.(ABSTRACT TRUNCATED AT 250 WORDS)
Phosphorothioate-modified oligodeoxyribonucleotides. III. NMR and UV spectroscoptc studies of theRp-Rp,Sp-Sp, andRp-Spduplexes, [d(GGsAATTCC)]2, derived from diastereomericO-ethyl phosphorothioates (1986)

2D-NOE and 1H NMR chemical shift data obtained for the title oligonucleotides were compared with similar data previously reported [Broido et al. (1985) Eur. J. Biochem. 150, 117-128] for the unmodified "parent" structure, [d(GGAATTCC)]2. The spectroscopically detectable structural perturbations caused by replacement of phosphate oxygen with sulfur were mostly localized within the GsA moiety, and were greater for the Rp configuration wherein sulfur is oriented into the major groove of the B-helix. UV-derived Tm measurements gave the following order of stability for the duplexes in 0.4 M NaCl: unmodified (33.9 +/- 0.1 degrees C) approximately Sp-Sp (34.1 degrees C) greater than Rp-Rp (31.7 degrees C). The title compounds were prepared by a new and convenient synthetic route which utilized HPLC to separate the diastereomeric O-ethyl phosphorothioate precursors, (Rp)- and (Sp)-d[GG(S,Et)AATTCC], for subsequent de-ethylation by ammonia in water.
Strategies to reduce late-stage drug attrition due to mitochondrial toxicity (2007)

Mitochondrial dysfunction is increasingly implicated in the etiology of drug-induced toxicities and negative side-effect profiles. Early identification of mitochondrial liabilities for new chemical entities is therefore crucial for avoiding late-stage attrition during drug development. Limitations of traditional methods for assessing mitochondrial dysfunction have discouraged routine evaluation of mitochondrial liabilities. To circumvent this bottleneck, a high-throughput screen has been developed that measures oxygen consumption; one of the most informative parameters for the assessment of mitochondrial status. This technique has revealed that some, but not all, members of many major drug classes have mitochondrial liabilities. This dichotomy encourages optimism that efficacy can be disassociated from mitochondrial toxicity, resulting in safer drugs in the future.
Neuropsychological prediction of dementia and the absence of dementia in healthy elderly persons (1994)

Identification of elderly individuals with low and high risk for future dementia has emerged as an important clinical and public health issue. To address this issue, we assessed neuropsychological performance in 317 initially nondemented elderly persons between 75 and 85 years of age and followed them for at least 4 years as part of the Bronx Aging Study. Four measures of cognitive function from the baseline assessment (delayed recall from the Buschke Selective Reminding Test, recall from the Fuld Object Memory Evaluation, the Digit Symbol subtest from the Wechsler Adult Intelligence Scale, and a verbal fluency score) can identify one subgroup with an 85% probability of developing dementia over 4 years and another with a 95% probability of remaining free of dementia. The model achieved an overall positive predictive value of 68%, or three times the base rate, for prediction of the development of dementia in our sample. The overall negative predictive value for prediction of absence of dementia was 88%. Baseline measures of cognitive function, often performed many years before the actual diagnosis of dementia, can provide important information about dementia risk. The group likely to develop dementia becomes a target for preventive or early therapeutic interventions, and the group unlikely to develop dementia can be reassured.
Leakage current modeling of series-connected thin film transistors (1995)

The leakage current of an arbitrary number of series-connected polysilicon Thin Film Transistors (TFTs) with a common gate is shown to be easily computed from the I-V characteristics of a single FET for the first time, both by an analytical model and by graphical techniques. Good agreement with experimental data is obtained for drain biases greater than /spl sim/1 V. The work is also applicable to single crystal Silicon-On-Insulator (SOI) TFTs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ImageNet: A large-scale hierarchical image database (2009)

The explosion of image data on the Internet has the potential to foster more sophisticated and robust models and algorithms to index, retrieve, organize and interact with images and multimedia data. But exactly how such data can be harnessed and organized remains a critical problem. We introduce here a new database called “ImageNet”, a large-scale ontology of images built upon the backbone of the WordNet structure. ImageNet aims to populate the majority of the 80,000 synsets of WordNet with an average of 500–1000 clean and full resolution images. This will result in tens of millions of annotated images organized by the semantic hierarchy of WordNet. This paper offers a detailed analysis of ImageNet in its current state: 12 subtrees with 5247 synsets and 3.2 million images in total. We show that ImageNet is much larger in scale and diversity and much more accurate than the current image datasets. Constructing such a large-scale database is a challenging task. We describe the data collection scheme with Amazon Mechanical Turk. Lastly, we illustrate the usefulness of ImageNet through three simple applications in object recognition, image classification and automatic object clustering. We hope that the scale, accuracy, diversity and hierarchical structure of ImageNet can offer unparalleled opportunities to researchers in the computer vision community and beyond.
Una familia de estimadores de escala mediante truncamientos (2003)

This first example of a logic model for patient portals shows how health IT planning and evaluation may benefit from logic models.
Directed Inhibition of Nuclear Import in Cellular Hypertrophy (2001)

Each nuclear pore is responsible for both nuclear import and export with a finite capacity for bidirectional transport across the nuclear envelope. It remains poorly understood how the nuclear transport pathway responds to increased demands for nucleocytoplasmic communication. A case in point is cellular hypertrophy in which increased amounts of genetic material need to be transported from the nucleus to the cytosol. Here, we report an adaptive down-regulation of nuclear import supporting such an increased demand for nuclear export. The induction of cardiac cell hypertrophy by phenylephrine or angiotensin II inhibited the nuclear translocation of H1 histones. The removal of hypertrophic stimuli reversed the hypertrophic phenotype and restored nuclear import. Moreover, the inhibition of nuclear export by leptomycin B rescued import. Hypertrophic reprogramming increased the intracellular GTP/GDP ratio and promoted the nuclear redistribution of the GTP-binding transport factor Ran, favoring export over import. Further, in hypertrophy, the reduced creatine kinase and adenylate kinase activities limited energy delivery to the nuclear pore. The reduction of activities was associated with the closure of the cytoplasmic phase of the nuclear pore preventing import at the translocation step. Thus, to overcome the limited capacity for nucleocytoplasmic transport, cells requiring increased nuclear export regulate the nuclear transport pathway by undergoing a metabolic and structural restriction of nuclear import.
Physical and mechanical properties of soy protein‐based plastic foams (1999)

Abstract Flexible plastic foams using soy protein isolate (SPI), soy protein concentrate (SPC), and defatted soy flour (DFS) were produced by interacting proteins with glycerol‐propylene oxide polyether triol (polyol), surfactant, triethanolamine (crosslinking agents), tertiary amine (catalyst), and water (blowing agent). The density, compressive stress, resilience, and dimensional stability of foams with SPI, SPC, and DFS increased as the initial concentration of soy protein increased. The foam density increased with increasing weight percentage of SPI, SPC, and DFS. The resilience values of SPI containing foam increased with the increasing addition of SPI up to a maximum 30% SPI addition. An increase in SPI up to 20% caused an increase in the compressive stress (225 kPa) in comparison to control polyurethane foam (187 kPa). The control foam and foam containing 20% DFS had a similar load‐deformation relationship. The foam containing 20% SPI and SPC also exhibited a similar shape, but with a higher compressive stress. The compressive stress of all foams was steeply increased after 55% strain, since the foams completely collapsed upon compression.
Macrophage activation syndrome: a potentially fatal complication of rheumatic disorders (2001)

MAS is a rare and potentially fatal complication of childhood rheumatic disorders. Most of our patients were female, and most cases were preceded by infection. Bone marrow studies support the diagnosis. Deranged renal function may be a poor prognostic sign. Aggressive early therapy is essential.
Housing and Population Health: A review of the Literature (1999)

Report submitted to Canada Mortgage and Housing Corporation by Centre for Applied Social Research Faculty of Social Work, University of Toronto