gebhart/patrepeval huggingface dataset:
Pancreatic Differentiation of Stem Cells Reveals Pathogenesis of a Syndrome of Ketosis-Prone Diabetes (2021)

Genetic analysis of an adult patient with an unusual course of ketosis-prone diabetes (KPD) and lacking islet autoantibodies demonstrated a nucleotide variant in the 5'-untranslated region (UTR) of <i>PDX1</i>, a β-cell development gene. When differentiated to the pancreatic lineage, his induced pluripotent stem cells stalled at the definitive endoderm (DE) stage. Metabolomics analysis of the cells revealed that this was associated with leucine hypersensitivity during transition from the DE to the pancreatic progenitor (PP) stage, and RNA sequencing showed that defects in leucine-sensitive mTOR pathways contribute to the differentiation deficiency. CRISPR/Cas9 manipulation of the <i>PDX1</i> variant demonstrated that it is necessary and sufficient to confer leucine sensitivity and the differentiation block, likely due to disruption of binding of the transcriptional regulator NFY to the <i>PDX1</i> 5'-UTR, leading to decreased PDX1 expression at the early PP stage. Thus, the combination of an underlying defect in leucine catabolism characteristic of KPD with a functionally relevant heterozygous variant in a critical β-cell gene that confers increased leucine sensitivity and inhibits endocrine cell differentiation resulted in the phenotype of late-onset β-cell failure in this patient. We define the molecular pathogenesis of a diabetes syndrome and demonstrate the power of multiomics analysis of patient-specific stem cells for clinical discovery.
Array and statistical signal processing (2014)

This third volume, edited and authored by world leading experts, gives a review of the principles, methods and techniques of important and emerging research topics and technologies in array and statistical signal processing. With this reference source you will: * Quickly grasp a new area of research * Understand the underlying principles of a topic and its application* Ascertain how a topic relates to other areas and learn of the research issues yet to be resolved * Quick tutorial reviews of important and emerging topics of research in array and statistical signal processing* Presents core principles and shows their application* Reference content on core principles, technologies, algorithms and applications* Comprehensive references to journal articles and other literature on which to build further, more specific and detailed knowledge* Edited by leading people in the field who, through their reputation, have been able to commission experts to write on a particular topic
Degenerative changes of the canine cervical spine after discectomy procedures, an in vivo study (2017)

Discectomies lead to terminal degenerative changes. Therefore, these procedures should be indicated with caution specifically when performed for prophylactic purposes.
Phosphate Inhibits Acetotrophic Methanogenesis on Rice Roots (2000)

The contribution of acetate- and H(2)/CO(2)-dependent methanogenesis to total CH(4) production was determined in excised washed rice roots by radiolabeling, methyl fluoride inhibition, and stable carbon isotope fractionation. Addition of > or = 20 mM phosphate inhibited methanogenesis, which then was exclusively from H(2)/CO(2). Otherwise, acetate contributed about 50 to 60% of the total methanogenesis, demonstrating that phosphate specifically inhibited acetotrophic methanogens on rice roots.
Speed of low-frequency sound through lungs of normal men (1983)

The speed of propagation of vesicular lung sound through the lung has not been clearly established. In a recent study (J. Appl. Physiol.: Respirat. Environ. Exercise Physiol. 54: 304-308, 1983), Rice measured the speed of sound through the parenchyma of excised horse lungs and found it to be 25-70 m/s (less than 20% the speed of sound in air). Filling the lung with helium or sulfur hexafluoride changed the speed of transmission by less than 10%, indicating nongas propagation. The present study was designed to measure the speed of sound through human lungs in vivo. Five healthy, nonsmoking males (aged 27-38 yr) were studied. A microphone was placed on the neck beneath the larynx and another at each of eight locations on the chest wall. Measurements were made at functional residual capacity. White noise was band-pass filtered between 125 and 500 Hz, amplified, and delivered to a loudspeaker connected to a mouthpiece. The speed of sound was measured by cross-correlation analysis of the signals simultaneously detected by the tracheal and chest microphones. This was done after breathing both air and a mixture of 80% He in 20% O2 (He-O2). With air, the mean sound-transit time (trachea to chest wall) ranged from 2 ms at the upper chest to 5 ms at the lower chest (speed of approximately 30 m/s). With He-O2 the mean speed increased by only 10%, whereas the predicted increase of sound speed through gas alone would be greater than 100%. These results are consistent with the in vitro findings of Rice and suggest that within the frequency range of vesicular lung sounds transmission of sound introduced at the mouth is predominantly through the lung parenchyma, not through the airways.
32 Disease outcomes and care fragmentation in systemic lupus erythematosus (sle) (2017)

<h3>Background and Aims</h3> To examine the impact of care fragmentation across multiple healthcare institutions on disease outcomes in patients with systemic lupus erythematosus (SLE). <h3>Methods</h3> Methods: Using the Chicago HealthLNK Data Repository (HDR), an assembly of electronic health records from six institutions, we identified patients with SLE, using ICD-9 codes, whose care was delivered at more than one organisation. We examined whether patients had severe infections or comorbidities (ICD-9 code defined) that indicate SLE-induced damage. T-tests and chi-squared tests were used to examine differences between fragmentation groups. Logistic regression was used to assess factors contributing to the occurrence of disease outcomes. <h3>Results</h3> We identified 4276 patients with SLE. 856 (20%) received care from more than one healthcare institution. African American patients and patients with public insurance were more likely to experience care fragmentation compared to white and private insurance patients (OR 1.66; 95% CI 1.44, 1.97 and OR 1.63; 95% CI 1.42, 1.95). We identified increased risk of infections (OR 1.57; 95% CI 1.30, 1.88), cardiovascular disease (OR 1.51; 95% CI 1.23, 1.86), end stage renal disease (OR 1.34; 95% CI 1.05, 1.70), nephritis (OR 1.28; 95% CI 1.07, 1.54) and stroke (OR 1.28; 95% CI 1.01, 1.62) among patients with fragmented care, adjusted for age, sex, race, insurance status, length of follow-up time, and total visit count. <h3>Conclusion</h3> In this cross-site cohort of SLE patients, care fragmentation is associated with increased risk of severe infection and comorbidities. These results suggest that improved health information exchange could positively impact outcomes for SLE patients.
Classical and surround receptive field structure in cortical area MT as revealed by reverse correlation - eScholarship (2008)

This dissertation is organized into two main parts: physiology and new techniques. The physiology is organized into classical receptive fields, surround properties and global object selectivity of area MT. The first two physiology chapters used a novel sparse motion stimulus to drive MT cells and used reverse correlation to analyze the data. For the classical receptive field the spike triggered average was used as an estimate of the field. For the surround, maximally informative dimension analysis as originally developed by Sharpee at el. (2004) and further optimized for the stimulus distribution was used in these studies (see Chapter 5). Chapter 6 covers a circular statistic derived for use in Chapter 2. Using a new motion reverse correlation technique, we obtained high -resolution measurements of receptive field properties - spatial and directional selectivity - within cortical visual area MT. The standard, often implicit, view of these receptive fields is that they cover a contiguous area of the visual field and that the preferred direction is homogenous across this field. Contrary to this, we found that the receptive fields of many (19%) neurons were significantly patchy and that only half (48%) preferred only a single direction of motion within their receptive field. Both the spatial patchiness and directional preference variation were validated in single cells using more traditional stimuli. In the second chapter we used a variant of Maximally Informative Dimension (MID; Sharpee et al. 2004; Chapter 5) in order to find mechanisms that are not directly implied by the Spike Triggered Average (STA). Using MID we found a second kernel (receptive field, RF2) that interacted with the STA. We found 3 categories for RF2 structure : Surround Suppression, Off Preferred Direction Suppression and Omni-modulation. A divisive nonlinearity is found to fit the surround and off preferred direction suppression data well. In the third chapter we studied the response of area MT to a motion capture illusion. We first demonstrated a large psychophysical effect for humans, and then tested area MT's response to this stimulus. We found no modulation in area MT consistent with the global object motion, i.e. consistent with the illusion
Relationship between Classic Physiological Variables and Running Performance in Recreational Runners (2018)

The purpose of this study was to investigate the relationship between classic physiological variables [maximal oxygen uptake (VO2max), %VO2max at anaerobic threshold (AT), and running economy (RE)] and running performance in recreational runners. 39 recreational runners (24 males and 15 females) underwent a treadmill running test to determine the classic physiological variables and velocity at AT (vAT). AT was defined as the point at which the respiratory exchange ratio stabilized above 1.0, and it was used as an indirect performance variable. Multiple regression analysis showed that 94% of vAT values were explained by all classic physiological variables (p<0.001). In addition, all variables were significantly explanatory (VO2max, p<0.001; %VO2max at AT, p<0.001; and RE, p<0.001). In total, 35 subjects had completed a marathon within the past year. For these subjects, single regression analysis was performed, which showed that 67% of recent marathon times was explained by vAT (r=0.82, p<0.05). This study indicated that during a treadmill running test, VO2max, %VO2max at AT, and RE can precisely explain vAT, which is highly correlated with recent marathon times.
99th Dahlem Conference on Infection, Inflammation and Chronic Inflammatory Disorders: Induction and control of regulatory T cells in the gastrointestinal tract: consequences for local and peripheral immune responses (2010)

Regulatory T cells play a crucial role in normal gut homeostasis, as well as during infection with microbial or parasitic pathogens. Prior to infection, interactions with the commensal microflora are essential to differentiation of a healthy steady-state level of immunoregulation, mediated through both Toll-like receptor-dependent and -independent pathways. The ingress of pathogenic organisms may, according to the context, promote or reverse the regulatory environment, with onward consequences for inflammation in both the intestinal and extra-intestinal settings. Appropriate regulation of gut immunity thus depends upon a complex three-way interplay between host cells, commensals and pathogens, and can exert a major impact on systemic responses including allergy and autoimmunity.
Increase of etch resistance of deep ultraviolet photoresist by implantation (1999)

Ion implantation causes damage to photoresist and brings about the formation of a carbonized layer on the surface of the resist. The relationship between the extent of damage and the etch resistance of the resist was investigated. Four ion species, namely, Si, P, As, and BF2 were used. Heavier ions and higher implant energies generally increase the extent of damage and the density of the carbonized layer. Compared to a fresh resist, the formation of a dense carbonized layer increases the etch resistance whereas the formation of a porous carbonized layer decreases the etch resistance.
Shear-wave speeds and elastic moduli for different liquids. Part 2. Experiments (1986)

In this paper we describe the experimental apparatus that we use to measure transit speeds. Tables of measured values of transit speeds and the corresponding values of the shear modulus are presented. The criteria we use to determine if a transit speed is a shear-wave speed are described and applied to the data. The main criteria are that transit speeds should be independent of the gap size and the corresponding value of the shear modulus should be consistent with independent rheometrical measurements. All the elastic liquids and many liquids that are usually assumed to be Newtonian satisfy our criteria for shear waves. We present evidence that the measured wave speeds are associated with slower-relaxing molecular structures in the liquids.
Novel Therapeutic Approach for Neurodegenerative Pathologies: Multitarget Iron-Chelating Drugs Regulating Hypoxia-Inducible Factor 1 Signal Transduction Pathway (2011)

Our novel multimodal brain-permeable iron-chelating compounds M30 and HLA20 were demonstrated to possess neuroprotective/neurorescue activities in vitro and in vivo against several insults applicable to various neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Neuroprotection by iron chelators has been widely recognized with respect to their ability to prevent reactive oxygen species generation in the Fenton reaction by sequestering redox-active iron. An additional neuroprotective mechanism of iron-chelating compounds is associated with their ability to regulate the transcriptional activator hypoxia-inducible factor 1 (HIF-1). HIF-1 is a 'master switch' being an important physiological response mechanism, likely enhancing neuroprotective compensatory pathways involved in many physiological processes within the brain. This mini-review will discuss the multifunctional mechanisms of action of the drugs, M30 and HLA20 in preclinical models of neurodegeneration with a specific emphasis on their ability to activate the HIF-1 signal transduction pathway.
Rheumatologie heute – dynamisch zum Wohle der Patienten (2011)

Drug Prescribing for Patients with Chronic Kidney Disease in General Practice: a Cross-Sectional Study
Interactive Educational Tool for Memory Testing (2006)

Memories are one of the most important components in digital systems like SoCs. The high density of their cell array makes memories extremely vulnerable to physical defects. Hence, memory testing and Design-for-Test became one of the crucial tasks in the design of complex and heterogeneous SoCs. Politecnico di Torino and the Institute of Informatics have a wide experience in the field of RAM testing (i.e., automatic march test generation, fault simulators, memory BIST generators etc.). This work is a tentative to put the joint experience of our research groups in developing an interactive educational tool for the students that should introduce standard and well-known methods of memory testing based on BIST. The MemBIST Java Applet and the March Test Generator were two individual tools designed and implemented at the two mentioned institutions. They were merged into one tool in order to facilitate its usage also by the professionals
A nuclear protein tyrosine phosphatase is required for the inactivation of Stat1 (1999)

The Stat1 activation-inactivation cycle involves phosphorylation of Stat1 in the cytoplasm, translocation to the nucleus, and then a return of the protein to the cytoplasm in a dephosphorylated state. However, the intracellular site of Stat1 dephosphorylation has not been determined. As receptor signaling declines, the flow of activated Stat1 molecules should be to the site of their dephosphorylation. We found that upon receptor-Janus kinase inactivation, either gradual or abruptly induced by staurosporine treatment, the flow of Stat1 was from cytoplasm to the nucleus and the nucleus was the final compartment in which phosphorylated Stat1 was detected. N-terminal mutants of Stat1, previously shown to remain phosphorylated for a longer time than wild-type Stat1, were able to enter the nucleus and were not inactivated in the presence of staurosporine, directly demonstrating that these mutations affect phosphatase access and/or activity during the normal dephosphorylation of Stat1. In the presence of sodium vanadate, a phosphatase inhibitor, phosphorylated Stat1 accumulated in the nucleus as the total amount of Stat1 in the cytoplasm declined to low levels. We conclude that the nucleus is the site of Stat1 inactivation and that dephosphorylation is required for the rapid nuclear export of Stat1.
Investigation on Magnetic Torque Sensor using FeCoV Magnetic Wire (2021)

The purpose of this report is to produce a torque sensor that detects the torque applied to a minute diameter. A jig was manufactured to apply torque to a sample with a wire diameter of several mm. When various torques are applied to two FeCoV magnetic samples (φ8.5 mm and φ4.0 mm), the induced voltage tended to increase only for the sample of φ 4.0 mm. Reading this change may be applicable to a torque sensor that can detect the torque applied to a minute diameter.
Experiments with the Tangora 20,000 word speech recognizer (2005)

The Speech Recognition Group at IBM Research in Yorktown Heights has developed a real-time, isolated-utterance speech recognizer for natural language based on the IBM Personal Computer AT and IBM Signal Processors. The system has recently been enhanced by expanding the vocabulary from 5,000 words to 20,000 words and by the addition of a speech workstation to support usability studies on document creation by voice. The system supports spelling and interactive personalization to augment the vocabularies. This paper describes the implementation, user interface, and comparative performance of the recognizer.
Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma (2018)

In fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2-10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution. These simulated dislodged states were experimentally captured by NMR. Modeling of the different conformations revealed no obvious steric interactions of the J-domain with the rest of the RIIβ holoenzyme.
Human micro-insemination by injection of single or multiple sperm: ultrastructure* (1989)

The process of micro-insemination by single or multiple sperm transfer into the perivitelline space (PVS) or by direct sperm injection into oocytes was examined by transmission electron microscopy. Spermatozoa from normal and oligozoospermic men were injected into oocytes, obtained from consenting IVF patients, mostly by zona-puncture using micromanipulators. Spermatozoa were washed by the Percoll or Ficoll methods and capacitated using Whittingham's T6 or modified Tyrode's medium or incubated in strontium medium before injection. The women were stimulated by three IVF methods and oocytes were recovered by laparoscopy or ultrasonography. Sixty-one oocytes were cultured in T6 or Ham's F-10 media (3-24 h) and were subjected to micromanipulation. Four oocytes were also studied after zona-drilling. Normal 2-pronuclear ova were developed after single-sperm transfer satisfying all morphological criteria of fertilization. Both monospermic and polyspermic fertilization resulted after multiple sperm transfer, indicating that a vitelline block to polyspermy may exist in humans. The majority of oocytes examined were unfertilized. Spermatozoa with intact or reacted acrosomes and those undergoing the acrosome reaction were found in the PVS and in the ooplasm. Abnormal spermatozoa were also seen in these locations. Quantitation of acrosomal status in 16 oocytes after multiple-sperm transfer, revealed that 24% of spermatozoa were acrosome-reacted or reacting in the PVS following Ficoll entrapment, while 76% of spermatozoa were intact (33% of these abnormal). Sperm transfer seemed to be the least invasive, while direct sperm injection was comparatively destructive to oocytes. Drilling with acid made larger breaches in the zona when compared with mechanical perforation and spermatozoa occasionally escaped through breaches. Three 2-pronuclear ova obtained after multiple sperm transfer have resulted in two pregnancies, in cases of severe oligozoospermia, during the course of this study.
Supplementary Figure 8 from Proteasome Inhibition Causes Regression of Leukemia and Abrogates BCR-ABL–Induced Evasion of Apoptosis in Part through Regulation of Forkhead Tumor Suppressors (2023)

Supplementary Figure 8 from Proteasome Inhibition Causes Regression of Leukemia and Abrogates BCR-ABL–Induced Evasion of Apoptosis in Part through Regulation of Forkhead Tumor Suppressors
Haptoglobin (HP), Transferrni (TF) and Group-Specific Component (GC) Subtype Distribution in Bantu-Speaking People from Malawi (1993)

A sample from Malawi was studied for the genetic markers haptoglobin (HP), group-specific component (GC) and transferrin (TF). The following allele frequencies were found. For HP: 1F = 0.355, 1S = 0.204, 2FS = 0.396, 2SS = 0.044; the allele 2FF was not observed. For GC: 1F = 0.814, 1S = 0.057, 2 = 0.079, 1A1 = 0.047, 2A1 = 0.0025. For TF: C1 = 0.894, C2 = 0.075, C3 = 0.0026, D1 = 0.029. The HP subtype distribution is among the first to be reported for African blacks.
Multilevel Modulation by LED Luminance Distribution for Optical Camera Communication (2018)

Multilevel modulation by LED luminance distribution is proposed and experimentally verified to increase signal-to-interference-plus-noise-ratio (SINR) for optical camera communication (OCC). LED luminance level is measured by number of white pixels on the LED image and calibrated. Error-free transmission of 64 quadrature amplitude modulation (QAM) is experimentally demonstrated up to a distance of 2.0 meter using 30-frame-per-second (fps) image sensor.
Structural Development in Hard Si-Based TiN Coatings as a Function of Temperature: A Comprehensive Study in Vacuum and in Air (2001)

Ti-Si-N coatings with various silicon contents have been prepared by r.f. sputtering and annealed in vacuum and air at temperatures of up to 1000°C. Phase assemblages following coating comprised fcc TiN and a (Ti, Si)N phase referred to as phase 2. Annealing in vacuum showed that recrystallisation occurred in order to relieve residual stresses developed during coating. As the silicon content was increased, the rate of stress relaxation decreased due to a) decreased atom mobility and b) initially coarser grain sizes, both of which decreased recrystallisation rates. For materials comprising TiN and phase 2, phase 2 decomposed during vacuum annealing. For pure phase 2 materials no such decomposition effects were observed. Annealing in air results in oxidation of the Ti-Si-N coatings to TiO 2 and SiO 2 . As the silicon content is increased, the oxidation resistance improves until an optimum level of Si is exceeded, when it decreases again (see [1, 2] also).