gebhart/patrepeval huggingface dataset:
An Animal Training Model for Endoscopic Treatment of Zenkerʼs Diverticulum (2006)

Purpose: Zenker's Diverticulum (ZD) is an uncommon disease typically treated surgically. The surgical alternative is a diverticulotomy performed endoscopically. Given the rarity of this condition it is not possible to obtain training. There has been no animal model identified which resembles the disease in humans. We aim to present an animal model of ZD which resembles the disease in humans. Methods: We prospectively characterized the endoscopic, radiographic and histologic anatomy of the hypopharyngeal pouch in the pig. Domestic pigs scheduled for euthanasia underwent radiography, endoscopy and neck dissection within 20 minutes of euthenasia. Thirteen consecutive female domestic pigs weighing 29 to 66 kg were studied. The animals were initially studied under general anesthesia with orotracheal intubation and then euthenized. Pictures were taken for the endoscopic view as well as X-rays during barium swallow in one pig. The neck region was dissected and the pharynx and upper esophagus were extracted. The size of the pouch was measured and the block fixed in formalin. Fixed specimens were cut in the transverse and longitudinal axis. The septum between the pouch and the esophagus was reviewed microscopically. Results: The pouch measured an average of 2.7 cm (1.3 to 5 cm), depending on the size of the pig. From an endoscopic (Figure 1: esophageal lumen upper half of image; hypopharyngeal pouch lower half of image) and radiologic perspective (Figure 2) it is identical to a ZD. The septum contains muscle as well as fibrous tissue and fat. These anatomical characteristics resemble closely the anatomy in humans.FigureFigureConclusions: Based upon our observations and anatomic study, we postulate that the domestic pig serves as a natural model resembling ZD. We believe to have established an animal training model for the endoscopic treatment of ZD. [figure1] [figure2]
The influence of femoral internal and external rotation on cartilage stresses within the patellofemoral joint (2008)

Internal and external rotation of the femur plays an important role in defining the orientation of the patellofemoral joint, influencing contact areas, pressures, and cartilage stress distributions. The purpose of this study was to determine the influence of femoral internal and external rotation on stresses in the patellofemoral cartilage. We constructed finite element models of the patellofemoral joint using magnetic resonance (MR) images from 16 volunteers (8 male and 8 female). Subjects performed an upright weight-bearing squat with the knee at 60 degrees of flexion inside an open-MR scanner and in a gait laboratory. Quadriceps muscle forces were estimated for each subject using an electromyographic-driven model and input to a finite element analysis. Hydrostatic and octahedral shear stresses within the cartilage were modeled with the tibiofemoral joint in a "neutral" position and also with the femur rotated internally or externally by 5 degrees increments to +/-15 degrees . Cartilage stresses were more sensitive to external rotation of the femur, compared with internal rotation, with large variation across subjects. Peak patellar shear stresses increased more than 10% with 15 degrees of external rotation in 75% of the subjects. Shear stresses were higher in the patellar cartilage compared to the femoral cartilage and patellar cartilage stresses were more sensitive to femoral rotation compared with femoral cartilage stress. Large variation in the cartilage stress response between individuals reflects the complex nature of the extensor mechanism and has clinical relevance when considering treatment strategies designed to reduce cartilage stresses by altering femoral internal and external rotation.
Performance of jet substructure techniques for large-R jets in proton-proton collisions at $ \sqrt{s}=7 $ TeV using the ATLAS detector (2013)

A bstract This paper presents the application of a variety of techniques to study jet substructure. The performance of various modified jet algorithms, or jet grooming techniques, for several jet types and event topologies is investigated for jets with transverse momentum larger than 300 GeV. Properties of jets subjected to the mass-drop filtering, trimming, and pruning algorithms are found to have a reduced sensitivity to multiple proton-proton interactions, are more stable at high luminosity and improve the physics potential of searches for heavy boosted objects. Studies of the expected discrimination power of jet mass and jet substructure observables in searches for new physics are also presented. Event samples enriched in boosted W and Z bosons and top-quark pairs are used to study both the individual jet invariant mass scales and the efficacy of algorithms to tag boosted hadronic objects. The analyses presented use the full 2011 ATLAS dataset, corresponding to an integrated luminosity of 4.7 ± 0.1 fb −1 from proton-proton collisions produced by the Large Hadron Collider at a centre-of-mass energy of $ \sqrt{s}=7 $ TeV.
Challenging aspects of contemporary cochlear implant electrode array design (2017)

Lateral wall arrays are less likely to cause trauma to cochlear structures. As the current trend in cochlear implantation is the maximal protection of residual acoustic hearing, the lateral wall arrays seem more suitable for hearing preservation CI surgeries. Future development could focus on combining the advantages of both types: perimodiolar location in the basal turn extended to lateral wall location for higher turn locations.
[Barrett's esophagus. Characterization and monitoring policy]. (1991)

The authors review the literature about the assessment of risks of adenocarcinoma occurring over the natural history of Barrett's oesophagus with an incidence much higher than in the general population. The best marker is histological analysis of the cylindric epithelium for signs of dysplasia or early carcinoma. Although there is much controversy about the practical benefit of regular surveillance, the authors recommend a yearly endoscopy with multiple site biopsies. With the new potent drugs aimed at controlling gastro-oesophageal reflux, regression of metaplasia might occur, as the authors have observed in 3 patients treated by 60 mg omeprazole. However, prospective studies are needed to confirm this finding and its possible effect on reducing the risk of adenocarcinoma.
Fully selective intramolecular ortho photocycloaddition of 4-(4-methoxy-phenoxy)-3-(N3-benzoylthymin-1-yl)but-1- ene: an unprecedented benzene–thymine photocycloaddition (1997)

On irradiation of 4-(4-methoxyphenoxy)-3-(N 3 -benzoylthymin-1-yl)but-1-e ne 1 at 254 nm in THF a single photoadduct 2 is formed as a result of chemo-, regio- and stereo-selective intramolecular ortho photocycloaddition of the thymine double bond to the 1,2-positions of the phenyl ring.
User-feedback and optimization for multi-view calibration (2013)

Multi-view camera calibration is an essential task in the filed of 3D reconstruction which holds especially for immersive media applications like 3D videocommunication. Although the problem of multi-view calibration is basically solved, there is still space to improve the calibration process and to increase the accuracy during acquisition of calibration patterns. It is commonly known that robust and accurate calibration requires feature points that are equally distributed in 3D space covering the whole volume of interest. In this paper, we propose a user guided calibration based on a graphical user interface, which drastically simplifies the correct acquisition of calibration patterns. Based on an optimized selection of patterns and their corresponding feature points, the multi-view calibration becomes much faster in terms of data acquisition as well as computational effort by reaching the same accuracy with standard unguided acquisitions of calibration pattern.
Figure S5 from Oral IRAK-4 Inhibitor CA-4948 Is Blood-Brain Barrier Penetrant and Has Single-Agent Activity against CNS Lymphoma and Melanoma Brain Metastases (2023)

&lt;p&gt;Supplemental Figure 5: Chromatogram of CA-4948.&lt;/p&gt;
Gait and Lower Extremity Kinematic Analysis as an Outcome Measure After Femoroacetabular Impingement Surgery (2014)

Level IV, systematic review of Level IV studies.
Renal Functional Reserve in Pregnancy (1988)

Creatinine clearance has been evaluated under baseline conditions and after acute protein load in five normal and 29 pregnant women at different stages of pregnancy without evidence of renal disease. After a 3-h period in which creatinine clearance was measured hourly (resting GFR), a meal containing 80 g of proteins was administered and creatinine clearance was measured hourly for 4 h (test GFR). Resting GFR in normal subjects averaged 104 +/- 22.5 ml/min per 1.73 m2, the wide variation being due to different dietary, protein intake (from 0.3 to 1.2 g of protein per kg body weight). In the pregnant women the resting GFR increased progressively from the first month (99.8 +/- 12.8 ml/min per 1.73 m2) to the last month of gestation (149.6 +/- 12.5 ml/min per 1.73 m2). All subjects showed a significant increase of GFR after protein load although the greatest difference between the resting and the test GFR was detected in the first trimester. Inulin clearance was also measured in seven subjects after protein loading to compare creatinine and inulin clearance values. The two clearance values did not differ significantly, showing that creatinine can be safely used as a reliable marker for measuring GFR. Test GFR averaged 163.3 +/- 4.1 ml/min per 1.73 in normal subjects and 163.8 +/- 6.5 ml/min per 1.73 m2 in pregnant women without any relationship with the stage of pregnancy. The identity of test GFR both in normal subjects and in pregnant women suggests that this parameter is likely to be related to the functioning renal mass, and represents the filtration capacity of the kidney.(ABSTRACT TRUNCATED AT 250 WORDS)
Pathology of Long-Chain 3-Hydroxyacyl-Coa Dehydrogenase Deficiency Caused by the G1528C Mutation (1997)

Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency is a recently discovered disorder affecting the mitochondrial beta-oxidation of fatty acids. There have been few reports of the pathologic findings in beta-oxidation defects. We examined pathologic specimens from 16 patients with this disorder (11 patients were homozygous for the common mutation G1528C, 5 patients were siblings with a similar clinical presentation). Autopsies were performed on all 15 patients who died, and liver biopsy specimens were available from 8 patients. Hepatomegaly and steatosis of the liver, found in every patient, were often combined with fibrosis or cirrhosis. Cardiomegaly and accumulation of fat in the myocardium, renal tubules, and skeletal muscle were found in many patients. A detailed neuropathologic examination was performed on six patients, and brain specimens obtained at autopsy were examined in four others. In general, neuropathologic findings were mild and unspecific, but vacuolization was detected in the deep gray matter and in the cerebellum and brain stem nuclei of five patients. In one patient the vacuolization was prominent; in the other four it was milder and more focal. The vacuoles seemed to be either in the neuropil or associated with swollen hydropic cells. The uniform pattern of histopathologic changes facilitates the diagnostics in this severe disorder, allowing opportunities for therapy and prenatal diagnosis.
Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease (2020)

The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn’s disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities.
Noise exposure when drilling at the round window niche – A temporal bone study (2023)

Introduction Enlarging the round window niche by drilling is a routine surgical procedure of cochlear implantation (CI). Bone vibrations induced by drilling, especially near the cochlea, are regarded a great risk for hearing impairment of the patients. In this study we measured drilling induced noise exposure with an acceleration sensor at the patients head. Since it is not possible to place the sensor near the cochlear, a correction strategy has been developed to evaluate the noise exposure when drilling at the round window niche.
Toward A Vaccine for AIDS: The Emergence of Immunobiology-Based Vaccine Development (1994)

Over a decade has passed since the identification of the human immunodeficiency virus (HIV) as the causative agent of AIDS. During this time, HIV has been extensively characterized, and a variety of vaccine constructs and strategies have been explored. For the most part, these have been driven by successes of the past with other pathogens, or by novel approaches enabled by technologies of the present. With the maturing of our insights into the immunopathology of HIV and basic immunological mechanisms, we are presented with unprecedented opportunities to rationally develop vaccine approaches strategically designed to counter the immunopathology of HIV. As opposed to absolute prevention of infection, the primary goal of these strategies may be to limit infection and to assure a response to infection that prevents disease and transmission. Thus, such vaccines may find utility in both preventive and therapeutic roles. In this paper, we present the background and current state of immunobiology-driven vaccine development for AIDS.
Blind PARAFAC receivers for DS-CDMA systems (2000)

This paper links the direct-sequence code-division multiple access (DS-CDMA) multiuser separation-equalization-detection problem to the parallel factor (PARAFAC) model, which is an analysis tool rooted in psychometrics and chemometrics. Exploiting this link, it derives a deterministic blind PARAFAC DS-CDMA receiver with performance close to non-blind minimum mean-squared error (MMSE). The proposed PARAFAC receiver capitalizes on code, spatial, and temporal diversity-combining, thereby supporting small sample sizes, more users than sensors, and/or less spreading than users. Interestingly, PARAFAC does not require knowledge of spreading codes, the specifics of multipath (interchip interference), DOA-calibration information, finite alphabet/constant modulus, or statistical independence/whiteness to recover the information-bearing signals. Instead, PARAFAC relies on a fundamental result regarding the uniqueness of low-rank three-way array decomposition due to Kruskal (1977, 1988) (and generalized herein to the complex-valued case) that guarantees identifiability of all relevant signals and propagation parameters. These and other issues are also demonstrated in pertinent simulation experiments.
Conservation of the structure and function of bacterial tryptophan synthases (2019)

Tryptophan biosynthesis is one of the most characterized processes in bacteria, in which the enzymes from <i>Salmonella typhimurium</i> and <i>Escherichia coli</i> serve as model systems. Tryptophan synthase (TrpAB) catalyzes the final two steps of tryptophan biosynthesis in plants, fungi and bacteria. This pyridoxal 5'-phosphate (PLP)-dependent enzyme consists of two protein chains, α (TrpA) and β (TrpB), functioning as a linear αββα heterotetrameric complex containing two TrpAB units. The reaction has a complicated, multistep mechanism resulting in the β-replacement of the hydroxyl group of l-serine with an indole moiety. Recent studies have shown that functional TrpAB is required for the survival of pathogenic bacteria in macrophages and for evading host defense. Therefore, TrpAB is a promising target for drug discovery, as its orthologs include enzymes from the important human pathogens <i>Streptococcus pneumoniae</i>, <i>Legionella pneumophila</i> and <i>Francisella tularensis</i>, the causative agents of pneumonia, legionnaires' disease and tularemia, respectively. However, specific biochemical and structural properties of the TrpABs from these organisms have not been investigated. To fill the important phylogenetic gaps in the understanding of TrpABs and to uncover unique features of TrpAB orthologs to spearhead future drug-discovery efforts, the TrpABs from <i>L. pneumophila</i>, <i>F. tularensis</i> and <i>S. pneumoniae</i> have been characterized. In addition to kinetic properties and inhibitor-sensitivity data, structural information gathered using X-ray crystallo-graphy is presented. The enzymes show remarkable structural conservation, but at the same time display local differences in both their catalytic and allosteric sites that may be responsible for the observed differences in catalysis and inhibitor binding. This functional dissimilarity may be exploited in the design of species-specific enzyme inhibitors.
The sonochemical and microwave-assisted synthesis of nanosized YAG particles (2005)

Nanoparticles of YAG were prepared by sonochemistry and by microwave radiation. In both cases, the last stage of the preparation was annealing at a high temperature, which led to a highly aggregated product. To reduce the aggregation we have added κ-carrageenan (a sugar) to the reaction mixture. The effect of the sugar is presented and discussed herein.
A 125 mm/sup 2/ 1Gb NAND flash memory with 10 MB/s program throughput (2003)

A 125 mm/sup 2/ 1Gb NAND flash uses 0.13 /spl mu/m CMOS. The cell is 0.077 /spl mu/m/sup 2/. Chip architecture is changed to reduce chip size and to realize 10.6 MB/s throughput for program and 20 MB/s for read. An on-chip page copy function provides 9.4 MB/s throughput for garbage collection.
Parametric X-ray Study from Textured Molybdenum Polycrystal (2006)

We performed a systematic study on Parametric X-ray radiation from a textured polycrystalline molybdenum target at a 150-MeV electron ring. The measurements were conducted at three observation angles (11.27, 25.89, and 179.85°). The spectral data shows that the spectrum has a unique characterestics: its peak energies depend mainly on the observation angles, its width is much wider than that with the monocrystal case, and its intensities are sometimes comparable to the charactestics Kα of Mo. The observed properties are related to the texture of the polycrystal.
Neuromedin U receptors (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database (2019)

Neuromedin U receptors (provisional nomenclature as recommended by NC-IUPHAR [29]) are activated by the endogenous 25 amino acid peptide neuromedin U (neuromedin U-25, NmU-25), a peptide originally isolated from pig spinal cord [90]. In humans, NmU-25 appears to be the sole product of a precursor gene (NMU, P48645) showing a broad tissue distribution, but which is expressed at highest levels in the upper gastrointestinal tract, CNS, bone marrow and fetal liver. Much shorter versions of NmU are found in some species, but not in human, and are derived at least in some instances from the proteolytic cleavage of the longer NmU. Despite species differences in NmU structure, the C-terminal region (particularly the C-terminal pentapeptide) is highly conserved and contains biological activity. Neuromedin S (neuromedin S-33) has also been identified as an endogenous agonist [95]. NmS-33 is, as its name suggests, a 33 amino-acid product of a precursor protein derived from a single gene and contains an amidated C-terminal heptapeptide identical to NmU. NmS-33 appears to activate NMU receptors with equivalent potency to NmU-25.
Mitochondrial Dysfunction in Skeletal Muscle of Amyloid Precursor Protein-overexpressing Mice (2012)

Inclusion body myositis, the most common muscle disorder in the elderly, is partly characterized by abnormal expression of amyloid precursor protein (APP) and intracellular accumulation of its proteolytic fragments collectively known as β-amyloid. The present study examined the effects of β-amyloid accumulation on mitochondrial structure and function of skeletal muscle from transgenic mice (MCK-βAPP) engineered to accumulate intramyofiber β-amyloid. Electron microscopic analysis revealed that a large fraction of myofibers from 2-3-month-old MCK-βAPP mice contained numerous, heterogeneous alterations in mitochondria, and other cellular organelles. [(1)H-decoupled](13)C NMR spectroscopy showed a substantial reduction in TCA cycle activity and indicated a switch from aerobic to anaerobic glucose metabolism in the MCK-βAPP muscle. Isolated muscle fibers from the MCK-βAPP mice also exhibited a reduction in cytoplasmic pH, an increased rate of ROS production, and a partially depolarized plasmalemma. Treatment of MCK-βAPP muscle cells with Ru360, a mitochondrial Ca(2+) uniporter antagonist, reversed alterations in the plasmalemmal membrane potential (V(m)) and pH. Consistent with altered redox state of the cells, treatment of MCK-βAPP muscle cells with glutathione reversed the effects of β-amyloid accumulation on Ca(2+) transient amplitudes. We conclude that structural and functional alterations in mitochondria precede the reported appearance of histopathological and clinical features in the MCK-βAPP mice and may represent key early events in the pathogenesis of inclusion body myositis.
Mapping of a Region of Ebola Virus VP40 That Is Important in the Production of Virus‐Like Particles (2007)

Ebola virus VP40 contains 2 overlapping late domains (7-PTAP-10 and 10-PPEY-13) that are essential for its interaction with Tsg101 and Nedd4 in the promotion of viral egress. Deletion of the late domains inhibits VP40-induced virus-like particles (VLPs). However, a truncated form of VP40, which lacks a late domain because of the deletion of amino acids 1-30, is released into supernatant as a VLP, indicating that the remaining portion of VP40 contains the structural elements required for VLP release. Thus, the purpose of this study was to identify the VP40 sequence essential for VLP budding, through the generation of deletion and alanine-scanning mutants. We found that the amino acid sequence around the proline at position 53 plays a critical role in VLP production and intracellular transport. These data also may suggest that a novel host factor(s) is involved in virus budding.
Changes in gene expression profiles of multiple myeloma cells induced by arsenic trioxide (ATO): possible mechanisms to explain ATO resistance in vivo (2005)

Multiple myeloma (MM) is an incurable plasma cell malignancy marked by eventual resistance to therapy. Although arsenic trioxide (ATO) can induce apoptosis in MM cell lines, the in vivo activity of ATO in MM has been disappointing. The existence of ATO resistance mechanisms in MM can be inferred. We sought to generate hypotheses for ATO resistance by studying the gene expression profiles of MM cells that survived in culture with 0.5 micromol/l ATO. Among the 31 genes whose quantitative levels of expression (QLE) significantly increased in ATO were haem oxygenase 1 (HO-1) and metallothionein-2A (MT-2A). Among the 56 genes whose QLE were significantly decreased were genes that modulate cell cycling [BTBD2 and IGFBP7 (mac25)] and sensitivity to reactive oxygen species (ROS) (BACH2). HO-1 exerts an anti-apoptotic effect in ischaemic cells, and MT-2A chelates ATO intracellularly. Inhibition of HO-1 with tin protoporphyrin enhances ROS in MM cells in ATO, and addition of N-acetylcysteine increases MT-2A. Protective antioxidant responses occur in MM cells exposed to ATO, and may occur in stromal cells as well, and act to quench ROS and provide diffusible anti-apoptotic factors. They may also involve cysteine-rich proteins that chelate ATO and modulate redox-sensitive residues on proteins, such as nuclear factor kappa B and p53. A better understanding of ATO resistance will enable ATO to be combined with other agents for MM.