gebhart/patrepeval huggingface dataset:
Wave-based sound propagation in large open scenes using an equivalent source formulation (2013)

We present a novel approach for wave-based sound propagation suitable for large, open spaces spanning hundreds of meters, with a small memory footprint. The scene is decomposed into disjoint rigid objects. The free-field acoustic behavior of each object is captured by a compact per-object transfer function relating the amplitudes of a set of incoming equivalent sources to outgoing equivalent sources. Pairwise acoustic interactions between objects are computed analytically to yield compact inter-object transfer functions. The global sound field accounting for all orders of interaction is computed using these transfer functions. The runtime system uses fast summation over the outgoing equivalent source amplitudes for all objects to auralize the sound field for a moving listener in real time. We demonstrate realistic acoustic effects such as diffraction, low-passed sound behind obstructions, focusing, scattering, high-order reflections, and echoes on a variety of scenes.
The Ubiquitin Binding Region of the Smurf HECT Domain Facilitates Polyubiquitylation and Binding of Ubiquitylated Substrates (2009)

Mono- and polyubiquitylation of proteins are key steps in a wide range of biological processes. However, the molecular mechanisms that mediate these different events are poorly understood. Here, we employed NMR spectroscopy to map a non-covalent ubiquitin binding surface (UBS) on the Smurf ubiquitin ligase HECT domain. Analysis of mutants of the HECT UBS reveal that interfering with the UBS surface blocked Smurf-dependent degradation of its substrate RhoA in cells. In vitro analysis revealed that the UBS was not required for UbcH7-dependent charging of the HECT catalytic cysteine. Surprisingly, although the UBS was required for polyubiquitylation of both Smurf itself and the Smurf substrate RhoA, it was not required for monoubiquitylation. Furthermore, we show that mutating the UBS interfered with efficient binding of a monoubiquitylated form of RhoA to the Smurf HECT domain. Our findings suggest the UBS promotes polyubiquitylation by stabilizing ubiquitylated substrate binding to the HECT domain.
The Influence of Stoma Occlusion on Aspects of Tracheoesophageal Voice (1998)

In this study, speech of 21 laryngectomized patients is investigated under 2 different stoma occlusion conditions, i.e. direct digital occlusion of the stoma (by thumb or finger), and digital occlusion (by finger) via a special heat and moisture exchanger with speech valve (Provox Stomafilter). For both conditions, acoustical analyses of voice quality (various pitch, amplitude, tremor and harmonicity measures) were performed on a sustained /a/, the mean maximum phonation time was calculated, and a phonetogram was made. Acoustical analysis was possible in 13 of the 21 voices (for the other voices, the pitch was too low or the voice was too aperiodic), but no statistical significant differences were found for any of the acoustical parameters studied. However, the maximum phonation time was significantly longer, and the dynamic range significantly larger, under the Stomafilter occlusion condition. The maximum phonation time showed a relevant improvement in 57% of the patients, while the dynamic range showed a relevant improvement in 35% of the patients. In total, 75% of the patients experience an improvement in one or both of these speech characteristics when using the Stomafilter occlusion. It can be concluded that optimal stoma occlusion by means of a specialized device has a positive influence on two relevant parameters of prosthetic voice production: maximum phonation time and dynamic loudness range.
Congenital insensitivity to pain with anhidrosis (CIPA): Novel mutations of theTRKA (NTRK1) gene, a putative uniparental disomy, and a linkage of the mutantTRKA andPKLR genes in a family with CIPA and pyruvate kinase deficiency (2001)

Congenital insensitivity to pain with anhidrosis is an autosomal recessive hereditary disorder characterized by recurrent episodic fever, anhidrosis (inability to sweat), absence of reaction to noxious stimuli, self-mutilating behavior, and mental retardation. The human TRKA gene (NTRK1), located on chromosome 1q21-q22 encodes the receptor tyrosine kinase for nerve growth factor. We reported that TRKA is the gene responsible for CIPA and we developed a comprehensive strategy to screen for TRKA mutations and polymorphisms, as based on the gene's structure and organization. Here we report eight novel mutations detected as either a homozygous or heterozygous state in nine CIPA families from five countries. Mendelian inheritance of the mutations was confirmed in seven families for which samples from either parent were available. However, non-mendelian inheritance seems likely for the family when only samples from the mother and siblings, (but not from the father) were available. A paternal uniparental disomy for chromosome 1 is likely to be the cause of reduction to homozygosity of the TRKA gene mutation in this family. Interestingly, a Hispanic patient from the USA has two autosomal genetic disorders, CIPA and pyruvate kinase deficiency, whose genetic loci are both mapped to a closely linked chromosomal region. A splice mutation and a missense mutation were detected in the TRKA and PKLR genes from the homozygous proband, respectively. Thus, concomitant occurrence of two disorders is ascribed to a combination of two separate mutant genes, not a contiguous gene syndrome. This finding suggests a mechanism responsible for two autosomal genetic disorders in one patient. All these data further support findings that TRKA defects can cause CIPA in various ethnic groups. This will aid in diagnosis and genetic counseling of this painless but severe genetic disorder.
Beta 1 subunits of sodium channels. Studies with subunit-specific antibodies. (1990)

The purified Na+ channel from rat brain consists of alpha (260 kDa), beta 1 (36 kDa), and beta 2 (33 kDa) subunits. Pure beta 1 subunits were prepared from purified rat brain Na+ channels which had been adsorbed to hydroxylapatite resin and used to prepare specific anti-beta 1 subunit antiserum. Antibodies purified from this antiserum by antigen affinity chromatography immunoprecipitate 125I-labeled, purified beta 1 subunits and purified Na+ channels (measured as high affinity [3H] saxitoxin binding sites) and recognize beta 1 subunits on immunoblots of solubilized rat brain membranes. The affinity-purified anti-beta 1 antibodies recognize beta 1 subunits in rat spinal cord, heart, skeletal muscle, and sciatic nerve, but do not detect immunoreactive beta 1 subunits in eel electroplax or eel brain. The developmental time course of expression of immunoreactive beta 1 subunits in rat forebrain was measured by immunoprecipitation followed by immunoblotting with affinity-purified anti-beta 1 antibodies. The amount of immunoreactive beta 1 subunits increased steadily to adult levels during the first 21 days of postnatal development.
Molecular architecture of a light-harvesting antenna. Structure of the 18 S core-rod subassembly of the Synechococcus 6301 phycobilisome. (1983)

The 18 S subassembly particles obtained by partial dissociation of phycobilisomes from Synechococcus 6301 (Anacystis nidulans) strain AN 112 contain approximately one-half of the mass of the phycobilisome and include core-rod junctions (Yamanaka, G., Lundell, D. J., and Glazer, A. N. (1982) J. Biol. Chem. 257, 4077-4086). The polypeptide composition of 18 S complexes, determined by analysis of uniformly 14C-labeled phycobilisomes, gave the following stoichiometry: 75K:27K:18.3K:alpha beta allophycocyanin monomer: alpha beta phycocyanin monomer of 1:2:1:5:6; where 75K, 27K, etc. represent polypeptides of 75, 27 kilodaltons, etc. The 18.3K polypeptide is a hitherto underscribed biliprotein bearing a single phycocyanobilin. The NH2-terminal sequence of this subunit was determined to be homologous to that of the beta subunit of allophycocyanin. Chromatography of products resulting from limited trypsin treatment of the 18 S complex led to the isolation of three subcomplexes: a mixture of (alpha beta)3 . 22K and (alpha beta)3 . 24K phycocyanin complexes, an (alpha beta)3 allophycocyanin trimer, and an (alpha beta)2 . 18.3K.40K.11K allophycocyanin-containing complex. The 22K and 24K components were products of the degradation of the 27K polypeptides, whereas the 40K and 11K components were derived from the 75K polypeptide. The subcomplexes accounted for the composition of the 18 S complex. Determination of the composition, stoichiometry, and spectroscopic properties of the subcomplexes has led to a model of the polypeptide arrangement within the 18 S complex and of the pathway of energy transfer among these polypeptides.
Nociceptive cutaneous stimuli evoke localized contractions in a skeletal muscle (1988)

1. The cutaneus trunci muscle (CTM) is a thin broad sheet of skeletal muscle that originates bilaterally on the humerus and inserts beneath the dermis of back and flank skin. A nociceptive stimulus applied to the skin elicits a localized reflex contraction in that region of the CTM underlying the site of sensory stimulation. While this "local sign" character of the CTM reflex corresponds to the segmental distribution of the afferent nerves (the dorsal cutaneous nerves, or DCNs) that enter the spinal cord in the lower thoracic and the lumbar levels, the motor output originates entirely from a circumscribed region of the cervical spinal cord. 2. Electrophysiological analysis of EMG activity in the muscle reflexly evoked by direct electrical stimulation of individual DCNs revealed a distinct topographic relationship, in that the shortest latency response of EMG activity in the muscle was consistently located approximately 1.0 cm rostral to the dermatome of the stimulated DCN. 3. Histochemical studies of the CTM show that individual muscle fibers run rostrocaudally, are focally innervated, and in adult rats, are approximately 3.0 cm in length. The major motor nerves exit from the brachial plexus, and functionally they divide the muscle into longitudinal (rostrocaudal) territories, which thus lie orthogonal to the dermatomal pattern of sensory innervation. The localized reflex responses to focal sensory stimuli indicate that the major longitudinal muscle fields contain many "reflex compartments." 4. The compartmentalized nature of the reflex response in the CTM suggests that nociceptive input from any one sensory dermatome has a preferred access to that fraction of the motoneuron pool that supplies the area of muscle underlying that specific region of skin, i.e., there is a sort of "matching" between groups of primary sensory neurons, interneurons, and motoneurons, which relates to the peripheral location of the stimulated nerve endings and of the muscle fibers that are reflexly activated. Although the partitioning of sensory input to motor nuclei has been shown most clearly for monosynaptic Ia connections, the CTM reflex suggests that sensory partitioning may also be demonstrated in a polysynaptic circuit.
FGFR1 Is Essential for Prostate Cancer Progression and Metastasis (2013)

The fibroblast growth factor receptor 1 (FGFR1) is ectopically expressed in prostate carcinoma cells, but its functional contributions are undefined. In this study, we report the evaluation of a tissue-specific conditional deletion mutant generated in an ARR2PBi(Pbsn)-Cre/TRAMP/fgfr1(loxP/loxP) transgenic mouse model of prostate cancer. Mice lacking fgfr1, in prostate cells developed smaller tumors that also included distinct cancer foci still expressing fgfr1 indicating focal escape from gene excision. Tumors with confirmed fgfr1 deletion exhibited increased foci of early, well-differentiated cancer and phyllodes-type tumors, and tumors that escaped fgfr1 deletion primarily exhibited a poorly differentiated phenotype. Consistent with these phenotypes, mice carrying the fgfr1 null allele survived significantly longer than those without fgfr1 deletion. Most interestingly, all metastases were primarily negative for the fgfr1 null allele, exhibited high FGFR1 expression, and a neuroendocrine phenotype regardless of fgfr1 status in the primary tumors. Together, these results suggest a critical and permissive role of ectopic FGFR1 signaling in prostate tumorigenesis and particularly in mechanisms of metastasis.
Advanced Micro-Lithography Process with Chemical Shrink Technology (2001)

We have developed an advanced micro-lithographic process for producing 0.1 µm contact holes (CH). A chemical shrink technology, resolution enhancement lithography assisted by chemical shrink (RELACS) utilizes the cross-linking reaction catalyzed by the acid component existing in a predefined resist pattern. This “RELACS” process is a hole shrinking procedure that includes simple coating, baking, and rinse steps applied after conventional photolithography. We evaluated the dependency of CH shrinkage on resist formulation. Though the acetal type KrF positive resist (low activation energy system) can achieve around 0.1 µm CH after RELACS processing under the optimized condition, the acrylate type positive resist (high activation energy system) showed less shrinkage under the same process condition. The shrinkage performance of the RELACS process largely depends on the resist chemistry used as the underlying layer. The results of these studies are discussed in terms of the influence of the base polymer on shrinkage performance and tendency.
The developmental toxicity of boric acid in mice, rats, and rabbits. (1994)

Boric acid (BA) is a naturally occurring agent used in manufacturing processes and numerous consumer products. Because of the potential for both industrial and consumer exposure to boron-containing compounds, and the lack of developmental toxicity data, the National Toxicology Program evaluated the potential for boric acid to cause developmental toxicity in pregnant Swiss (CD-1) mice, Sprague-Dawley rats (n = 26-28/group), and New Zealand rabbits (n = 18-23/group). BA was provided in the feed to mice and rats at 0, 0.1, 0.2, or 0.4% throughout gestation to attain steady-state exposure as early as possible during development. Average doses (mg/kg/day) were 248, 452, or 1003 for mice, and 78, 163, or 330 in rats. A separate group of rats received 0.8% BA in the feed, or 539 mg/kg/day only on gestation days (gd) 6 to 15. Rabbits were given BA (0, 62.5, 125, or 250 mg/kg) by gavage administration on gd 6 to 19. Maternal body weight, food and/or water consumption and signs of toxicity were monitored at regular intervals. At termination, gd 17 (mice), 20 (rats), or 30 (rabbits), the uterus was examined to determine the number of resorptions, dead, or live fetuses. Fetuses were weighed and live fetuses were examined for external, visceral, and skeletal defects. Mouse dams exhibited mild renal lesions (> or = 248 mg/kg/day BA), increased water intake and relative kidney weight (1003 mg/kg/day BA), and decreased weight gain during treatment.(ABSTRACT TRUNCATED AT 250 WORDS)
Constitutive endocytosis and recycling of major histocompatibility complex class II glycoproteins in human B-lymphoblastoid cells. (1992)

Cleavable cell surface radiolabelling reagents were used to measure the endocytosis and recycling of class II major histocompatibility complex (MHC) glycoproteins in human B-lymphoblastoid cells. It is shown that mature class II alpha beta dimers on the cell surface are constitutively endocytosed and that recycling can be demonstrated even from small endosomal pools. Endocytosis was blocked when cellular ATP levels were depleted or when clathrin polymerization was inhibited, implicating clathrin-coated pits in the endocytic process. Taken together with earlier studies, these results suggest that mature class II MHC molecules are constitutively endocytosed and recycled from acidic peripheral endosomes which may enhance their capacity to bind and present T cell epitopes which do not require processing.
Measurement of Lactose Repressor-Mediated Loop Formation and Breakdown in Single DNA Molecules (1995)

In gene regulatory systems in which proteins bind to multiple sites on a DNA molecule, the characterization of chemical mechanisms and single-step reaction rates is difficult because many chemical species may exist simultaneously in a molecular ensemble. This problem was circumvented by detecting DNA looping by the lactose repressor protein of Escherichia coli in single DNA molecules. The looping was detected by monitoring the nanometer-scale Brownian motion of microscopic particles linked to the ends of individual DNA molecules. This allowed the determination of the rates of formation and breakdown of a protein-mediated DNA loop in vitro. The measurements reveal that mechanical strain stored in the loop does not substantially accelerate loop breakdown, and the measurements also show that subunit dissociation of tetrameric repressor is not the predominant loop breakdown pathway.
i-bodies, Human Single Domain Antibodies That Antagonize Chemokine Receptor CXCR4 (2016)

CXCR4 is a G protein-coupled receptor with excellent potential as a therapeutic target for a range of clinical conditions, including stem cell mobilization, cancer prognosis and treatment, fibrosis therapy, and HIV infection. We report here the development of a fully human single-domain antibody-like scaffold termed an "i-body," the engineering of which produces an i-body library possessing a long complementarity determining region binding loop, and the isolation and characterization of a panel of i-bodies with activity against human CXCR4. The CXCR4-specific i-bodies show antagonistic activity in a range of in vitro and in vivo assays, including inhibition of HIV infection, cell migration, and leukocyte recruitment but, importantly, not the mobilization of hematopoietic stem cells. Epitope mapping of the three CXCR4 i-bodies AM3-114, AM4-272, and AM3-523 revealed binding deep in the binding pocket of the receptor.
Natural History of Community‐Acquired Methicillin‐ResistantStaphylococcus aureusColonization and Infection in Soldiers (2004)

CA-MRSA colonization with PVL-positive strains was associated with a significant risk of soft-tissue infection, suggesting that CA-MRSA may be more virulent than MSSA. Previous antibiotic use may play a role in CA-MRSA colonization.
Antisense PNA effects in Escherichia coli are limited by the outer-membrane LPS layer (2000)

Antisense peptide nucleic acids (PNAs) can inhibit Escherichia coli gene expression and cell growth through sequence-specific RNA binding, and this opens possibilities for novel anti-infective agents and tools for microbial functional genomics. However, the cellular effects of PNAs are limited relative to effects in cell extracts, presumably because of cell barrier components such as the outer-membrane lipopolysaccharide (LPS) layer or drug efflux pumps, both of which function to exclude antibiotics and other foreign molecules. To evaluate the importance of such cellular factors on PNA effects, the authors developed a positive assay for antisense inhibition by targeting the lac operon repressor and compared PNA susceptibilities in mutant and wild-type E. coli by assessing lacZ induction. Strains with defective LPS (AS19 and D22) were more permeable to the antibiotic nitrocefin and more susceptible to PNA than the wild-type. Also, PNA potency was improved in wild-type cells grown in the presence of certain cell-wall-permeabilizing agents. In contrast, the activities of the Acr and Emr drug efflux pumps were not found to affect PNA susceptibility. The results show that the LPS layer is a major barrier against cell entry, but PNAs that can enter E. coli are likely to remain active inside cells.
A Triage Metric for Determining the Extent of DCT-Based Compression Artifacts in a Digital Image (2002)

A triage metric is proposed to determine the extent of blocking and contouring artifacts in an image due to JPEG compression. It is found that this metric has a linear correlation with subjective judgements of print quality. This triage metric can be used to determine the amount of needed image enhancement or achieve a good trade-off between image quality and system throughput.
New Developments in Short-, Medium-, and Long-Radius Lateral Drilling (1989)

ABSTRACT While traditional definitions classify short-, medium- and long-radius lateral wells by angle build rates, the technology now employed to achieve those build rates suggests an industry definition which characterizes lateral wells not only in terms of wellbore geometry, but in engineering terms as well. In proposing such a definition, this paper examines new developments in downhole technology, focusing on short- and medium-radius systems to show how choice of drilling hardware can determine the type of curve drilled, as well as how it is planned and completed. New horizontal well-planning techniques developed in light of recent hardware improvements are also discussed, while technicaf innovations still in development are noted. Field results of recent lateral wells present examples of problem-solving, since a detailed discussion of lateral applications exceeds the scope of this paper. Concluding remarks suggest areas for further development to improve economics and performance in lateral drilling.
Three-dimensional photon counting double-random-phase encryption (2013)

In this Letter, we present a three-dimensional (3D) photon counting double-random-phase encryption (DRPE) technique using passive integral imaging. A 3D photon counting DRPE can encrypt a 3D scene and provides more security and authentications due to photon counting Poisson nonlinear transformation on the encrypted image. In addition, 3D imaging allows verification of the 3D object at different depths. Preliminary results and performance evaluation have been presented.
Nitric oxide-producing CD11b+Ly-6G(Gr-1)+CD31(ER-MP12)+cells in the spleen of cyclophosphamide–treated mice: implications for T-cell responses in immunosuppressed mice (2000)

During recovery from intensive chemotherapy with cyclophosphamide (CTX), mice suffer a severe but transitory impairment in spleen cell proliferation to T-cell mitogens (Con A or anti-CD3 plus IL-2). Although CTX treatment reduced spleen T-cell cellularity, this cannot fully account for T-cell unresponsiveness. The results showed that CTX induces the colonization of spleen by an immature myeloid CD11b+Ly-6G+CD31+ population. Its presence closely correlated with the maximum inhibition of T-cell proliferation. Moreover, this suppressive activity was dependent on nitric oxide (NO) production in cultures since (1) higher amounts of nitric oxide and inducible nitric oxide synthase (iNOS) mRNA were produced in CTX spleen cells (CTX-SC) than in control splenocyte cultures and (2) NOS inhibitors greatly improved the proliferation of T lymphocytes. Nitric oxide production and suppressive activity were also dependent on endogenous interferon-γ (IFN-γ) production since anti–IFN-γ abrogated both effects. Finally, iNOS protein expression was restricted to a heterogeneous population of CD31+cells in which CD11b+Ly-6G+ cells were required to suppress T-cell proliferation. These results indicated that CTX might also cause immunosuppression by a mechanism involving the presence of immature myeloid cells with suppressor activity. This may have implications in clinical praxis since inappropriate immunotherapies in patients treated with intensive chemotherapy could lead to deleterious T-cell responses. (Blood. 2000;95:212-220)