gebhart/patrepeval huggingface dataset:
Preparation, Characterization, and in Vivo Evaluation of an Oil Suspension of a Bovine Growth Hormone Releasing factor Analog (1996)

Pharmacia & Upjohn Inc. has discovered a superior bovine growth hormone releasing factor analog, [IIe2,Ser8,28,Ala15,Leu27,Hse30] bGRF (1-30)-NH-ethyl, acetate salt (U-90699F), for enhancement of animal growth. This report delineates the preparation, characterization, and in vivo evaluation of a U-90699F oil suspension. The oil suspension formulation was selected because of its simplicity, inexpensiveness, and ability to produce sustained U-90699F release. 40% U-90699F monomers were incorporated into Miglyol oil with acceptable injectability. Both reversed-phase-high-pressure liquid chromatography (RP-HPLC) and Fourier transform infrared spectroscopy (FTIR) were utilized to evaluate its chemical and structural stability. This suspension formulation demonstrated no significant changes in concentration as determined by RP-HPLC for 10 weeks at both 25 and 39 degrees C. The U-90699F dispersed in oil also showed no signs of structural conversion from alpha-helix to beta-sheet as monitored by FTIR. However, there was an increase in alpha-helix/disordered coil structure after initial drug incorporation. The suspension was subcutaneously administered to Holstein steers. Areas under the serum somatotropin concentration curve were used to determine the duration of action. It was found that the suspension was able to effectively elevate serum somatotropin for at least 14 days.
Mesenchymal stem cell-derived CCL-9 and CCL-5 promote mammary tumor cell invasion and the activation of matrix metalloproteinases (2013)

Stromal chemokine gradients within the breast tissue microenvironment play a critical role in breast cancer cell invasion, a prerequisite to metastasis. To elucidate which chemokines and mechanisms are involved in mammary cell migration we determined whether mesenchymal D1 stem cells secreted specific chemokines that differentially promoted the invasion of mammary tumor cells in vitro. Results indicate that mesenchymal D1 cells produced concentrations of CCL5 and CCL9 4- to 5-fold higher than the concentrations secreted by 4T1 tumor cells (P < 0.01). Moreover, 4T1 tumor cell invasion toward D1 mesenchymal stem cell conditioned media (D1CM), CCL5 alone, CCL9 alone or a combination CCL5 and CCL9 was observed. The invasion of 4T1 cells toward D1 mesenchymal stem CM was dose-dependently suppressed by pre-incubation with the CCR1/CCR5 antagonist met-CCL5 (P < 0.01). Furthermore, the invasion of 4T1 cells toward these chemokines was prevented by incubation with the broad-spectrum MMP inhibitor GM6001. Additionally, the addition of specific MMP9/MMP13 and MMP14 inhibitors prevented the MMP activities of supernatants collected from 4T1 cells incubated with D1CM, CCL5 or CCL9. Taken together these data highlight the role of CCL5 and CCL9 produced by mesenchymal stem cells in mammary tumor cell invasion.
Lattice-imposed geometry in metal–organic frameworks: lacunary Zn4O clusters in MOF-5 serve as tripodal chelating ligands for Ni2+ (2012)

The inorganic clusters in metal–organic frameworks can be used to trap metal ions in coordination geometries that are difficult to achieve in molecular chemistry. We illustrate this concept by using the well-known basic carboxylate clusters in Zn4O(1,4-benzenedicarboxylate)3 (MOF-5) as tripodal chelating ligands that enforce an unusual pseudo-tetrahedral oxygen ligand field around Ni2+. The new Ni-based MOF-5 analogue is characterized by porosity measurements and a suite of electronic structure spectroscopies. Classical ligand field analysis of the Ni2+ ion isolated in MOF-5 classifies the Zn3O(carboxylate)6 “tripodal ligand” as an unusual, stronger field ligand than halides and other oxygen donor ligands. These results may inspire the widespread usage of MOFs as chelating ligands for stabilizing site-isolated metal ions in future reactivity and electronic structure studies.
Branchio-oculo-facial syndrome: case report. (1999)

Branchio-oculo-facial (BOF) syndrome is a rare dominant autosomal disorder. Less than 50 cases have been reported up to now. We present a Chinese boy with BOF syndrome who has characteristic features of bilateral postauricular cervical branchial cysts, bilateral complete cleft of primary palate, bilateral lacrimal duct obstruction and bilateral low set ears with posterior rotation. His intelligence and growth were normal at the age of 7 years. This is the first case reported in Taiwan. The overlap between BOR syndrome and BOF syndrome include external ear abnormalities with hearing loss, lacrimal duct obstruction, branchial cleft remnants, and renal or ureteral defects. The relationship between these two syndromes is still unclear. Contiguous gene deletion phenomenon, different mutations in the same gene, or distinct entities all have been proposed. The literature was reviewed and discussed, especially the reports about the gene EYA1 (eyes absent-like 1), which is responsible for branchio-oto-renal syndrome. If we can detect mutations of EYA1 gene in BOF patients, this could be the key for solving the above debate.
BlueConnect: Decomposing all-reduce for deep learning on heterogeneous network hierarchy (2019)

As deep neural networks get more complex and input datasets get larger, it can take days or even weeks to train a deep neural network to the desired accuracy. Therefore, enabling distributed deep learning at a massive scale is critical since it offers the potential to reduce the training time from weeks to hours. In this article, we present BlueConnect, an efficient communication library for distributed deep learning that is highly optimized for popular GPU-based platforms. BlueConnect decomposes a single all-reduce operation into a large number of parallelizable reduce–scatter and all-gather operations to exploit the tradeoff between latency and bandwidth and adapt to a variety of network configurations. Therefore, each individual operation can be mapped to a different network fabric and take advantage of the best performing implementation for the corresponding fabric. According to our experimental results on two system configurations, BlueConnect can outperform the leading industrial communication library by a wide margin, and the BlueConnect-integrated Caffe2 can significantly reduce synchronization overhead by 87% on 192 GPUs for Resnet-50 training over prior schemes.
MR Imaging of Lumbar Juxtaarticular Cysts (1990)

Three surgically proven cases of lumbar extradural juxtaarticular cysts were examined by magnetic resonance (MR) imaging. The highly variable MR signal patterns are presented.
Response of Cotton (Gossypium hirsutum) to Preplant-Applied Hormone-Type Herbicides (1993)

In a 3-yr field study on a Bosket silt loam, dicamba (0.3 and 0.6 kg ai ha −1 ) and 2,4-D amine (0.6, 1.1, and 2.2 kg ae ha −1 ) were applied at 3, 9, and 16 d before planting cotton. Most treatments applied 3 or 9 d before planting caused cotton injury and yield reduction. Replanting was necessary when 2,4-D at 2.2 kg ha −1 was applied 9 d before planting, and all treatments except dicamba at 0.3 kg ha −1 when applied 3 d before planting.
Aminoglycoside nephrotoxicity: do time and frequency of administration matter? (2001)

Aminoglycosides remains the mainstay in the treatment of gram-negative infections despite their potential oto-and nephrotoxicity although alternatives with equal or better efficacy are available. Several approaches were investigated to decrease aminoglycosides nephrotoxicity. Among them, only the once-daily dosing of aminoglycosides has been brought to the clinic and physicians are now increasingly adopting this approach to reduce the toxicity of these agents. The incidence of aminoglycoside nephrotoxicity can be further reduced in view of the recent data on the circadian variations of their nephrotoxicity. In fact, it has been clearly demonstrated in both experimental animals and humans that the toxicity is maximal when the drug is injected during the rest period compared with the activity period. Thus, injecting aminoglycosides once-daily at the time of the lowest toxicity is actually the most interesting and clinically applicable approach to reduce aminoglycosides toxicity.
Elements of X-Ray Diffraction (1957)

1. Properties of X-rays. 2. Geometry of Crystals. 3. Diffraction I: Directions of Diffracted Beams. 4. Diffraction II: Intensities of Diffracted Beams. 5. Diffraction III: Non-Ideal Samples. 6. Laure Photographs. 7. Powder Photographs. 8. Diffractometer and Spectrometer. 9. Orientation and Quality of Single Crystals. 10. Structure of Polycrystalline Aggregates. 11. Determination of Crystal Structure. 12. Precise Parameter Measurements. 13. Phase-Diagram Determination. 14. Order-Disorder Transformation. 15. Chemical Analysis of X-ray Diffraction. 16. Chemical Analysis by X-ray Spectrometry. 17. Measurements of Residual Stress. 18. Polymers. 19. Small Angle Scatters. 20. Transmission Electron Microscope.
Ultrastructural and Biophysical Characterization of Hepatitis C Virus Particles Produced in Cell Culture (2010)

We analyzed the biochemical and ultrastructural properties of hepatitis C virus (HCV) particles produced in cell culture. Negative-stain electron microscopy revealed that the particles were spherical (∼40- to 75-nm diameter) and pleomorphic and that some of them contain HCV E2 protein and apolipoprotein E on their surfaces. Electron cryomicroscopy revealed two major particle populations of ∼60 and ∼45 nm in diameter. The ∼60-nm particles were characterized by a membrane bilayer (presumably an envelope) that is spatially separated from an internal structure (presumably a capsid), and they were enriched in fractions that displayed a high infectivity-to-HCV RNA ratio. The ∼45-nm particles lacked a membrane bilayer and displayed a higher buoyant density and a lower infectivity-to-HCV RNA ratio. We also observed a minor population of very-low-density, >100-nm-diameter vesicular particles that resemble exosomes. This study provides low-resolution ultrastructural information of particle populations displaying differential biophysical properties and specific infectivity. Correlative analysis of the abundance of the different particle populations with infectivity, HCV RNA, and viral antigens suggests that infectious particles are likely to be present in the large ∼60-nm HCV particle populations displaying a visible bilayer. Our study constitutes an initial approach toward understanding the structural characteristics of infectious HCV particles.
Pruning Convolutional Neural Networks for Resource Efficient Inference (2016)

We propose a new formulation for pruning convolutional kernels in neural networks to enable efficient inference. We interleave greedy criteria-based pruning with fine-tuning by backpropagation - a computationally efficient procedure that maintains good generalization in the pruned network. We propose a new criterion based on Taylor expansion that approximates the change in the cost function induced by pruning network parameters. We focus on transfer learning, where large pretrained networks are adapted to specialized tasks. The proposed criterion demonstrates superior performance compared to other criteria, e.g. the norm of kernel weights or feature map activation, for pruning large CNNs after adaptation to fine-grained classification tasks (Birds-200 and Flowers-102) relaying only on the first order gradient information. We also show that pruning can lead to more than 10x theoretical (5x practical) reduction in adapted 3D-convolutional filters with a small drop in accuracy in a recurrent gesture classifier. Finally, we show results for the large-scale ImageNet dataset to emphasize the flexibility of our approach.
Widespread plasticity in CTCF occupancy linked to DNA methylation (2012)

CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor.
Vogt-Koyanagi-Harada disease (2000)

Vogt-Koyanagi-Harada (VKH) disease affects primarily persons who are Asian, Latino, Native American, or Asian Indian. Women appear to be affected more commonly than men, and VKH disease may occur at all ages, including childhood. Experimental data continue to support an autoimmune etiology for VKH disease, directed most probably against an antigenic component of the melanocyte, possibly tyrosinase or a tyrosinase-related protein. The clinical diagnosis of VKH disease continues to be based on physical findings. Newer imaging modalities such as magnetic resonance imaging, indocyanine green angiography, and digital image analysis have not added appreciably to our understanding of the condition. First-line therapy consists of high-dose corticosteroids, with use of corticosteroid-sparing agents for resistant or recalcitrant disease. Complications are the main cause of reversible and irreversible vision loss, with subretinal fibrosis and choroidal neovascular membranes having particularly poor prognoses.
<title>Fish-eye lens camera nonlinear calibration for stereo vision system</title> (2000)

This paper presents an approach to calibrating a fish-eye lens camera with high accuracy for stereo vision to recover dense depth image. The camera model accounts for the fish-eye deformation and major sources of camera distortion including radial distortion, decentering distortion and thin prism distortion. We use nonlinear least-squares techniques to solve for the camera parameters that best project three-dimensional points of a calibration pattern onto intensity edges in an image of this pattern, without explicitly extracting the features such as corners, edges or points. The effectiveness of the proposed calibration method has been proved by experimentation.
Aggregate channel features for multi-view face detection (2014)

Face detection has drawn much attention in recent decades since the seminal work by Viola and Jones. While many subsequences have improved the work with more powerful learning algorithms, the feature representation used for face detection still can't meet the demand for effectively and efficiently handling faces with large appearance variance in the wild. To solve this bottleneck, we borrow the concept of channel features to the face detection domain, which extends the image channel to diverse types like gradient magnitude and oriented gradient histograms and therefore encodes rich information in a simple form. We adopt a novel variant called aggregate channel features, make a full exploration of feature design, and discover a multi-scale version of features with better performance. To deal with poses of faces in the wild, we propose a multi-view detection approach featuring score re-ranking and detection adjustment. Following the learning pipelines in Viola-Jones framework, the multi-view face detector using aggregate channel features shows competitive performance against state-of-the-art algorithms on AFW and FDDB test-sets, while runs at 42 FPS on VGA images.
Methane Drainage from the Mary Lee Coalbed, Alabama, Using Horizontal Drilling Techniques (1980)

ABSTRACT The Bureau of Mines has developed several techniques for draining methane from coalbeds in advance of mining. Drilling long horizontal holes from an underground location is one of these techniques which has been successfully demonstrated in the Pittsburgh and Sunnyside coalbeds. A similar project was successfully conducted in the Mary Lee coalbed at Jim Walter Resources Inc., No. 4 mine. In a year about 1.13 million m3 (40 MMcf) of methane was recovered from the coalbed.
Tumor-associated antigen 22-1-1 expression in the uterine cervical squamous neoplasias. (1998)

We have reported that a novel tumor-associated antigen (Ag), 22-1-1, was expressed in cancer cells derived mainly from the uterus and ovary [K. Sonoda et al., Cancer (Phila.), 77: 1501-1509, 1996]. The 22-1-1 Ag existed not only in adenocarcinomas but also in squamous cell carcinomas in the uterine cervix. Here, a relationship between tumor progression and invasion and 22-1-1 Ag expression was investigated in squamous cell neoplasms of the uterine cervix using immunohistochemical staining. The 22-1-1 Ag was not detected in normal uterine cervix (0 of 10 total cases) and dysplasias (0 of 47 total cases). However, 20% of carcinoma in situ (4 of 20 total cases) and 16.7% of microinvasive carcinomas (2 of 12 total cases) stained positively for 22-1-1 Ag. Moreover, areas depicting microinvasion on histology in uterine cancers (stage Ia) were more strongly stained than carcinoma in situ lesions. 22-1-1 Ag expression was found to be more frequent in invasive squamous cell carcinomas (82.6%; 57 of 69 total cases). The 22-1-1 Ag existed both in the cytoplasm and on the membrane of cancer cells. These findings suggest that 22-1-1 Ag expression might be related to tumor cell progression and invasion in the uterine cervical squamous cell epithelium.
Relative Cerebral Blood Volume Values to Differentiate High-Grade Glioma Recurrence from Posttreatment Radiation Effect: Direct Correlation between Image-Guided Tissue Histopathology and Localized Dynamic Susceptibility-Weighted Contrast-Enhanced Perfusion MR Imaging Measurements (2008)

rCBV measurements obtained by using DSC and the protocol we have described can differentiate HGG recurrence from PTRE with a high degree of accuracy.
Hypophosphatasia - pathophysiology and treatment. (2012)

Hypophosphatasia (HPP) is the inborn-error-of-metabolism caused by loss-of-function mutation(s) in the gene that encodes the tissue-nonspecific isozyme of alkaline phosphatase (TNAP). The disease has been classified according to patient age when the first signs and symptoms manifest; i.e., perinatal, infantile, childhood, adult HPP. Other types include odonto HPP and perinatal benign. Babies with the perinatal/infantile forms of HPP often die with severe rickets and respiratory insufficiency and sometimes hypercalcemia and vitamin B<sub>6</sub>-responsive seizures. The primary biochemical defect in HPP is a deficiency of TNAP activity that leads to elevated circulating levels of substrates, in particular inorganic pyrophosphate (PP<sub>i</sub>), a potent calcification inhibitor. To-date, the management of HPP has been essentially symptomatic or orthopedic. However, enzyme replacement therapy with mineral-targeting TNAP (sALP-FcD<sub>10</sub>, also known as ENB-0040 or asfotase alfa) has shown promising results in a mouse model of HPP (<i>Alpl<sup>-/-</sup></i> mice). Administration of mineral-targeting TNAP from birth increased survival and prevented the seizures, rickets, as well as all the tooth abnormalities, including dentin, acellular cementum, and enamel defects in this model of severe HPP. Clinical trials using mineral-targeting TNAP in children 3 years of age or younger with life-threatening HPP was associated with healing of the skeletal manifestations of HPP as well as improved respiratory and motor function. Improvement is still being observed in the patients receiving continued asfotase alfa therapy, with more than 3 years of treatment in some children. Enzyme replacement therapy with asfotase alfa has to-date been successful in patients with life-threatening HPP.
Chronic renal denervation prevents glomerular hyperfiltration in diabetic rats (2004)

Renal nerves appear to be significantly involved in the mediation of glomerular hyperfiltration in experimental DM. If the kidney is prevented from sympathetic nerve stimulation, structural changes due to early diabetic nephropathy, i.e. glomerular enlargement, are abolished.
Paper-Based Microfluidic Surface Acoustic Wave Sample Delivery and Ionization Source for Rapid and Sensitive Ambient Mass Spectrometry (2011)

A surface acoustic wave-based sample delivery and ionization method that requires minimal to no sample pretreatment and that can operate under ambient conditions is described. This miniaturized technology enables real-time, rapid, and high-throughput analysis of trace compounds in complex mixtures, especially high ionic strength and viscous samples that can be challenging for conventional ionization techniques such as electrospray ionization. This technique takes advantage of high order surface acoustic wave (SAW) vibrations that both manipulate small volumes of liquid mixtures containing trace analyte compounds and seamlessly transfers analytes from the liquid sample into gas phase ions for mass spectrometry (MS) analysis. Drugs in human whole blood and plasma and heavy metals in tap water have been successfully detected at nanomolar concentrations by coupling a SAW atomization and ionization device with an inexpensive, paper-based sample delivery system and mass spectrometer. The miniaturized SAW ionization unit requires only a modest operating power of 3 to 4 W and, therefore, provides a viable and efficient ionization platform for the real-time analysis of a wide range of compounds.
Novel compound heterozygous laminina2‐chain gene (LAMA2) mutations in congenital muscular dystrophy (1998)

The laminina2-chain gene (LAMA2) encodes a basal lamina protein, laminina2, known to be deficient in one form of congenital muscular dystrophy (CMD). In a laminina2 deficient-CMD patient, we screened the entire LAMA2 cDNA (9534bp) by reverse transcriptase polymerase chain reaction combined with single strand conformational polymorphism analysis. Direct sequencing of aberrant conformers in this patient revealed two loss-of-function mutations, consistent with autosomal recessive inheritance. The patient had two novel heterozygous mutations: (I) an exon 4 nonsense mutation caused by a G→A substitution at cDNA position 547, changing the TGG codon for tryptophan into a TGA stop codon (W166X) in the N-terminus domain VI; (ii) an exon 54 frameshift mutation due to a deletion of a nucleotide ‘C’ at cDNA position 7707 (S2553Y), resulting in a premature stop codon (V2587X) in exon 55 in the globular G domain of laminina2 at the C-terminus. These mutations cause a disruption of the open reading frame of LAMA2. The absence of laminina2 observed in the patient's muscle biopsy could result from diminished levels of the LAMA2 transcript. Alternatively, the mutations might lead to translation of a truncated laminina2. By either mechanism the phenotype of congenital muscular dystrophy is believed to be the result of disruption of linkage between the extracellular matrix and the dystrophin glycoprotein complex. Hum Mutat 12:135, 1998. © 1998 Wiley-Liss, Inc.