gebhart/patrepeval huggingface dataset:
Requirements for the internalization of a murine monoclonal antibody directed against the HER-2/neu gene product c-erbB-2. (1991)

A murine monoclonal antibody, TA1, is directed against an epitope on the extracellular domain of the HER-2/neu (c-erbB-2) gene product. Requirements for TA1-induced internalization of c-erbB-2 have been studied using the SKBr3 human breast cancer cell line and several rat fibroblast cell lines that express either wild-type or mutant human c-erbB-2. Internalization of TA1 was monitored by assaying protease-resistant uptake of 125I-labeled TA1, by electron microscopy of gold-labeled TA1, and by inhibition of clonogenic growth of cells incubated with TA1 that had been conjugated with blocked ricin. Similar rates of internalization of TA1 were observed in SKBr3 and in rat fibroblasts that expressed human c-erbB-2. The route of endocytosis was the same as that observed with antibodies against other membrane receptors. Anti-c-erbB-2 and anti-transferrin receptor cointernalized through clathrin-coated pits, coated vesicles, endosomes, and multivesicular bodies. Products of mutant c-erbB-2 that lacked a portion of the tyrosine kinase domain or that lacked most of the cytoplasmic domain were endocytosed in the presence of TA1 as promptly as the wild-type c-erbB-2 product. Slightly more rapid internalization of TA1 was observed in rat cells that expressed c-erbB-2 with a single point mutation in the transmembrane domain. Taken together, our data suggest that neither the intracytoplasmic domain nor receptor phosphorylation is required for antibody-mediated endocytosis of c-erbB-2.
Stage I and II Posterior Tibial Tendon Dysfunction Treated by a Structured Nonoperative Management Protocol: An Orthosis and Exercise Program (2006)

This study suggests that many patients with stage I and II posterior tibial tendon dysfunction can be effectively treated nonoperatively with an orthosis and structured exercises.
Television Captioning for the Deaf (1984)

At the end of 1971 although there were in the United States and Canada over 100 million television receivers in use, the hearing-impaired community had been largely deprived of the benefits of television programming. With the exception of some sports events, the sound portion of the program carries a significant part of the intelligence so that without it the program cannot be enjoyed. While the hearing-impaired can be served to a limited extent by the addition of "open captions" to programs, (sub-titles seen on all receivers), viewers with normal hearing find open captions distracting and therefore it is not a general solution to the problem.
Adoptive immunotherapy with murine tumor-specific T lymphocytes engineered to secrete interleukin 2. (1994)

Adoptive immunogene therapy of cancer is not widely studied, although it has been proposed as a promising strategy for cancer gene therapy. One of the major obstacles to this approach is the difficulty in introducing cytokine genes efficiently into T lymphocytes. In this report, we developed an adoptive immunotherapy model with murine tumor-specific cytotoxic T lymphocytes. By using an adenoviral vector, we achieved up to 100% gene transduction of murine T lymphocytes. Treatment of mice with the cytotoxic T lymphocytes genetically modified to produce interleukin 2 resulted in reduction of tumor metastasis and longer survival from intracerebral tumor death, providing a hopeful strategy for treatments of human cancers.
Dynamic V/sub TH/ scaling scheme for active leakage power reduction (2003)

We present a Dynamic V/sub TH/ Scaling (DVTS) scheme to save the leakage power during active mode of the circuit. The power saving strategy of DVTS is similar to that of the Dynamic V/sub DD/ Scaling (DVS) scheme, which adaptively changes the supply voltage depending on the current workload of the system. Instead of adjusting the supply voltage, DVTS controls the threshold voltage by means of body bias control, in order to reduce the leakage power. The power saving potential of DVTS and its impact on dynamic and leakage power when applied to future technologies are discussed. Pros and cons of the DVTS system are dealt with in detail. Finally, a feedback loop hardware for the DVTS which tracks the optimal V/sub TH/ for a given clock frequency, is proposed. Simulation results show that 92% energy savings can be achieved with DVTS for 70 nm circuits.
Reinvestigation of the crystal structure of diglycine hydrochloride (1992)

A reinvestigation of the crystal structure of diglycine hydrochloride, (NH 2 CH 2 COOH) 2 HCl, was carried out. The structure is orthorhombic, space group P 2 1 2 1 2 1 , with a = 5.2992(6), b = 8.083(2), c = 17.973(2) Å and Z = 4. Three-dimensional intensity data collected on a CAD 4 diffractometer using Cu Kα radiation was used for the structure elucidation and refinement. The final R value is 0.055 for 779 reflections. All the hydrogen atoms have been located in the present study. The glycine molecules are held together by a network of N – H … Cl, N – H … O and O – H … O hydrogen bonds. One of the glycine molecules exists as a zwitterion whereas the other one in the cationic form.
Sparse Autoencoder-Based Feature Transfer Learning for Speech Emotion Recognition (2013)

In speech emotion recognition, training and test data used for system development usually tend to fit each other perfectly, but further 'similar' data may be available. Transfer learning helps to exploit such similar data for training despite the inherent dissimilarities in order to boost a recogniser's performance. In this context, this paper presents a sparse auto encoder method for feature transfer learning for speech emotion recognition. In our proposed method, a common emotion-specific mapping rule is learnt from a small set of labelled data in a target domain. Then, newly reconstructed data are obtained by applying this rule on the emotion-specific data in a different domain. The experimental results evaluated on six standard databases show that our approach significantly improves the performance relative to learning each source domain independently.
The Chemistry of Commercial Continuous Glucose Monitors (2009)

The analytical methodologies of the continuous glucose monitors (CGMs) commercialized to date are described. The devices include two noninvasive products: the GlucoWatch (Cygnus, Redwood City, CA) G2 Biographer uses iontophoresis to obtain a sample and electrochemistry for glucose detection, and PENDRA (Pendragon Medical Ltd., Zurich, Switzerland) utilizes impedance spectroscopy. Three minimally invasive systems employ subcutaneous amperometric sensors-Guardian REAL-Time (Medtronic MiniMed, Sylmar, CA), DexCom STS-7 (DexCom, San Diego, CA), and FreeStyle Navigator (Abbott Diabetes Care, Alameda, CA). The GlucoDay (A. Menarini I.F.R. S.r.l., Florence, Italy) collects a sample with a minimally invasive microdialysis fiber and measures the glucose electrochemically.
Oxazolone Colitis: A Murine Model of  T Helper Cell Type 2 Colitis Treatable with Antibodies to Interleukin 4 (1998)

In this study we describe oxazolone colitis, a new form of experimental colitis. This model is induced in SJL/J mice by the rectal instillation of the haptenating agent, oxazolone, and is characterized by a rapidly developing colitis confined to the distal half of the colon; it consists of a mixed neutrophil/lymphocyte infiltration limited to the superficial layer of the mucosa which is associated with ulceration. Oxazolone colitis is a T helper cell type 2 (Th2)-mediated process since stimulated T cells from lesional tissue produce markedly increased amounts of interleukin (IL)-4 and IL-5; in addition, anti-IL-4 administration leads to a striking amelioration of disease, whereas anti-IL-12 administration either has no effect or exacerbates disease. Finally, this proinflammatory Th2 cytokine response is counterbalanced by a massive transforming growth factor-beta (TGF-beta) response which limits both the extent and duration of disease: lesional (distal) T cells manifest a 20-30-fold increase in TGF-beta production, whereas nonlesional (proximal) T cells manifest an even greater 40-50-fold increase. In addition, anti-TGF-beta administration leads to more severe inflammation which now involves the entire colon. The histologic features and distribution of oxazolone colitis have characteristics that resemble ulcerative colitis (UC) and thus sharply distinguish this model from most other models, which usually resemble Crohn's disease. This feature of oxazolone colitis as well as its cytokine profile have important implications to the pathogenesis and treatment of UC.
Identification of the Hepatitis C Virus RNA Replication Complex in Huh-7 Cells Harboring Subgenomic Replicons (2003)

Formation of a membrane-associated replication complex, composed of viral proteins, replicating RNA, and altered cellular membranes, is a characteristic feature of plus-strand RNA viruses. Here, we demonstrate the presence of a specific membrane alteration, designated the membranous web, that contains hepatitis C virus (HCV) nonstructural proteins, as well as viral plus-strand RNA, in Huh-7 cells harboring autonomously replicating subgenomic HCV RNAs. Metabolic labeling with 5-bromouridine 5'-triphosphate in the presence of actinomycin D revealed that the membranous web is the site of viral RNA synthesis and therefore represents the replication complex of HCV.
Identification of Molecular Tumor Markers in Renal Cell Carcinomas with TFE3 Protein Expression by RNA Sequencing (2013)

TFE3 translocation renal cell carcinoma (tRCC) is defined by chromosomal translocations involving the TFE3 transcription factor at chromosome Xp11.2. Genetically proven TFE3 tRCCs have a broad histologic spectrum with overlapping features to other renal tumor subtypes. In this study, we aimed for characterizing RCC with TFE3 protein expression. Using next-generation whole transcriptome sequencing (RNA-Seq) as a discovery tool, we analyzed fusion transcripts, gene expression profile, and somatic mutations in frozen tissue of one TFE3 tRCC. By applying a computational analysis developed to call chimeric RNA molecules from paired-end RNA-Seq data, we confirmed the known TFE3 translocation. Its fusion partner SFPQ has already been described as fusion partner in tRCCs. In addition, an RNA read-through chimera between TMED6 and COG8 as well as MET and KDR (VEGFR2) point mutations were identified. An EGFR mutation, but no chromosomal rearrangements, was identified in a control group of five clear cell RCCs (ccRCCs). The TFE3 tRCC could be clearly distinguished from the ccRCCs by RNA-Seq gene expression measurements using a previously reported tRCC gene signature. In validation experiments using reverse transcription-PCR, TMED6-COG8 chimera expression was significantly higher in nine TFE3 translocated and six TFE3-expressing/non-translocated RCCs than in 24 ccRCCs (P < .001) and 22 papillary RCCs (P < .05-.07). Immunohistochemical analysis of selected genes from the tRCC gene signature showed significantly higher eukaryotic translation elongation factor 1 alpha 2 (EEF1A2) and Contactin 3 (CNTN3) expression in 16 TFE3 translocated and six TFE3-expressing/non-translocated RCCs than in over 200 ccRCCs (P < .0001, both).
THE IMMUNOGENETICS OF HUMAN INFECTIOUS DISEASES (1998)

Twin and adoptee studies have indicated that host genetic factors are major determinants of susceptibility to infectious disease in humans. Twin studies have also found high heritabilities for many humoral and cellular immune responses to pathogen antigens, with most of the genetic component mapping outside of the major histocompatibility complex. Candidate gene studies have implicated several immunogenetic polymorphisms in human infectious diseases. HLA variation has been associated with susceptibility or resistance to malaria, tuberculosis, leprosy, AIDS, and hepatitis virus persistence. Variation in the tumor necrosis factor gene promoter has also been associated with several infectious diseases. Chemokine receptor polymorphism affects both susceptibility ot HIV-1 infection and the rate of progression to AIDS. Inactivating mutations of the gamma-interferon receptor lead to increased susceptibility to typical mycobacteria and disseminated BCG infection in homozygous children. The active form of vitamin D has immunomodulatory effects, and allelic variants of the vitamin D receptor appear to be associated with differential susceptibility to several infectious diseases. NRAMP1, a macrophage gene identified by positional cloning of its murine homologue, has been implicated in susceptibility to tuberculosis in Africans. Whole genome linkage analysis of multi-case families is now being used to map and identify new loci affecting susceptibility to infectious diseases. It is likely that susceptibility to most microorganisms is determined by a large number of polymorphic genes, and identification of these should provide insights into protective and pathogenic mechanisms in infectious diseases.
TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery (2014)

Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
The Strained η2‐NAmido−NPyridine Coordination of Aminopyridinato Ligands (2003)

Abstract This review gives an account of the syntheses and structures of group‐3 (including lanthanides), ‐4 and ‐5 metal complexes stabilised by strained η 2 ‐coordinated aminopyridinato ligands. Reactivity studies and catalytic applications of the coordination compounds are discussed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Isolation and expression of the Rhodobacter sphaeroides gene (pgsA) encoding phosphatidylglycerophosphate synthase (1996)

The Rhodobacter sphaeroides pgsA gene (pgsARs), encoding phosphatidylglycerophosphate synthase (PgsARs), was cloned, sequenced, and expressed in both R. sphaeroides and Escherichia coli. As in E. coli, pgsARs is located immediately downstream of the uvrC gene. Comparison of the deduced amino acid sequences revealed 41% identity and 69% similarity to the pgsA gene of E. coli, with similar homology to the products of the putative pgsA genes of several other bacteria. Comparison of the amino acid sequences of a number of enzymes involved in CDP-diacylglycerol-dependent phosphatidyltransfer identified a highly conserved region also found in PgsARs. The pgsARs gene carried on multicopy plasmids was expressed in R. sphaeroides under the direction of its own promoter, the R. sphaeroides rrnB promoter, and the E. coli lac promoter, and this resulted in significant overproduction of PgsARs activity. Expression of PgsARs activity in E. coli occurred only with the E. coli lac promoter. PgsARs could functionally replace the E. coli enzyme in both a point mutant and a null mutant of E. coli pgsA. Overexpression of PgsARs in either E. coli or R. sphaeroides did not have dramatic effects on the phospholipid composition of the cells, suggesting regulation of the activity of this enzyme in both organisms.
PET studies on the brain uptake and regional distribution of [11C]vinpocetine in human subjects (2002)

Vinpocetine, administered intravenously in humans, readily passes the blood-brain barrier and enters the brain. Its regional uptake and distribution in the brain is heterogeneous, indicating binding to specific sites. The brain regions showing increased uptake in the human brain correspond to those in which vinpocetine has been shown to induce elevated metabolism and blood flow. These observations support the hypothesis that vinpocetine has direct neuronal actions in the human brain.
Cytochalasin B inhibits morphogenetic movement and muscle differentiation of activin‐treated ectoderm in Xenopus (1999)

Xenopus ectodermal explants (animal caps) begin to elongate after treatment with the mesoderm inducing factor activin A. This phenomenon mimics the convergent extension of dorsal mesoderm during gastrulation. To analyze the relationship between elongation movement and muscle differentiation, animal caps were treated with colchicine, taxol, cytochalasin B and hydroxyurea (HUA)/aphidicolin following activin treatment. Cytochalasin B disrupted the organization of actin filaments and inhibited the elongation of the activin-treated explants. Muscle differentiation was also inhibited in these explants at the histologic and molecular levels. Colchicine and taxol, which are known to affect microtubule organization, had little effect on elongation of the activin-treated exp ants. Co-treatment with HUA and aphidicolin caused serious damage on the explants and they did not undergo elongation. These results suggest that actin filaments play an important role in the elongation movement that leads to muscle differentiation of activin-treated explants.
Face image analysis by unsupervised learning and redundancy reduction (1998)

In a task such as face recognition, much of the important information may be contained in the high-order relationships among the image pixels. Representations such as (197) and Holons (48) are based on Principal component analysis (PCA), which encodes the correlational structure of the input, but does not address high-order statistical dependencies such as relationships among three or more pixels. Independent component analysis (ICA) is a generalization of PCA which encodes the high-order dependencies in the input in addition to the correlations. Representations for face recognition were developed from the independent components of face images. The ICA representations were superior to PCA for recognizing faces across sessions and changes in expression.
ICA was compared to more than eight other image analysis methods on a task of recognizing facial expressions in a project to automate the Facial Action Coding System (62). These methods included estimation of optical flow; representations based on the second-order statistics of the full face images such Eigenfaces (47, 197) local feature analysis (156), and linear discriminant analysis (23); and representations based on the outputs of local filters, such as a Gabor wavelet representations (50, 113) and local PCA (153). The ICA and Gabor wavelet representations achieved the best performance of 96% for classifying 12 facial actions. Relationships between the independent component representation and the Gabor representation are discussed.
Temporal redundancy contains information for learning invariances. Different views of a face tend to appear in close temporal proximity as the person changes expression, pose, or moves through the environment. The final chapter modeled the development of viewpoint invariant responses to faces from visual experience in a biological system by encoding spatio-temporal dependencies. The simulations combined temporal smoothing of activity signals with Hebbian learning (72) in a network with both feed-forward connections and a recurrent layer that was a generalization of a Hopfield attractor network. Following training on sequences of graylevel images of faces as they changed pose, multiple views of a given face fell into the same basin of attraction, and the system acquired representations of faces that were approximately viewpoint invariant.
Ultrastructure of developing alveoli. I. The role of the interstitial fibroblast (1978)

Abstract We examined the ultrastructural features of postnatal alveolar septal formation in rats from birth to 28 days of age. At birth, the rat lung consists of large saccules with thick walls and cellular interstitium. Interstitial cells have large oval nuclei with scant cytoplasm containing few organelles and scattered lipid droplets. These cells appear to be poorly differentiated mesenchymal cells not engaged in active protein synthesis or secretion. Between 5 and 15 days of age, saccule walls thin and many new alveolar septa form. Two types of interstitial fibroblasts are present: one which appears at the tips of newly formed septa has the characteristics of a myofibroblast and appears to be engaged in synthesis and secretion of elastin; the other fibroblast appears at the base of new septa, is filled with lipid and contains few other cytoplasmic organelles. After 15 days of age, alveolar walls become thinner, few new septa form and interstitial fibroblasts begin to resemble the dormant type of fibroblasts seen at birth. Thus, the process of postnatal alveolarization of lung parenchyma involves differentiation of the interstitial fibroblast and elastogenesis. The factors which control this process, the precise role of elastogenesis in alveolar septal formation, the origin and fate of the lipid filled fibroblast and the ultimate fate of the myofibroblast remain to be determined.
<i>D</i>-Methionine Attenuates Inner Hair Cell Loss in Carboplatin-Treated Chinchillas (2000)

Carboplatin, a second-generation platinum-based antineoplastic drug, preferentially destroys inner hair cells (IHCs) in the chinchilla while sparing outer hair cells (OHCs). D-Methionine (D-Met), a sulfur-containing amino acid, has been shown to protect hair cells from cisplatin damage in rats, but its ability to protect IHCs from carboplatin damage has not yet been evaluated in the chinchilla. We tested whether D-Met would protect the hair cells in the chinchilla from carboplatin. Animals were divided into two groups: a control group that only received carboplatin (100 mg/kg, i.p.) and an experimental group that received 300 mg/kg D-Met (i.p.) 30 min before carboplatin treatment. Ototoxicity was assessed by measuring the amount of IHC and OHC loss. Average IHC loss in the group treated with D-Met was 62% compared with 84% in the untreated control group. Thus, D-Met causes a statistically significant reduction in IHC loss induced by carboplatin.