gebhart/patrepeval huggingface dataset:
Wafer fusion: A novel technique for optoelectronic device fabrication and monolithic integration (1990)

Centimeter-size single-crystal InP or GaAs wafers have been fused together entirely, face to face or side by side, after a heat treatment in a graphite/quartz reactor which can press the wafers together through differential thermal expansion. Diodes formed by fusing p- and n-type wafers showed normal current-voltage characteristics and light emission. Fusion between lattice-mismatched wafers (i.e., InP and GaAs) has also been demonstrated.
Read-Performance Optimization for Deduplication-Based Storage Systems in the Cloud (2014)

Data deduplication has been demonstrated to be an effective technique in reducing the total data transferred over the network and the storage space in cloud backup, archiving, and primary storage systems, such as VM (virtual machine) platforms. However, the performance of restore operations from a deduplicated backup can be significantly lower than that without deduplication. The main reason lies in the fact that a file or block is split into multiple small data chunks that are often located in different disks after deduplication, which can cause a subsequent read operation to invoke many disk IOs involving multiple disks and thus degrade the read performance significantly. While this problem has been by and large ignored in the literature thus far, we argue that the time is ripe for us to pay significant attention to it in light of the emerging cloud storage applications and the increasing popularity of the VM platform in the cloud. This is because, in a cloud storage or VM environment, a simple read request on the client side may translate into a restore operation if the data to be read or a VM suspended by the user was previously deduplicated when written to the cloud or the VM storage server, a likely scenario considering the network bandwidth and storage capacity concerns in such an environment. To address this problem, in this article, we propose SAR, an SSD (solid-state drive)-Assisted Read scheme, that effectively exploits the high random-read performance properties of SSDs and the unique data-sharing characteristic of deduplication-based storage systems by storing in SSDs the unique data chunks with high reference count, small size, and nonsequential characteristics. In this way, many read requests to HDDs are replaced by read requests to SSDs, thus significantly improving the read performance of the deduplication-based storage systems in the cloud. The extensive trace-driven and VM restore evaluations on the prototype implementation of SAR show that SAR outperforms the traditional deduplication-based and flash-based cache schemes significantly, in terms of the average response times.
Mechanosensitive Afferent Units in the Lumbar Posterior Longitudinal Ligament (2001)

Mechanosensitive units classified into Group III or Group IV and with a high mechanical threshold (>7.0 g) were thought to act as nociceptive units. All units identified in this study satisfied these criteria. Our result suggests that afferent fibers from the lumbar posterior longitudinal ligament have a principally nociceptive function.
Measurement of combing forces (1986)

Synopsis A double comb method has been developed for the determination of combing forces for hair tresses, and the effects of environmental humidity have been studied. The origin of the midlength and end-peak forces is discussed, and the contribution of comb-hair friction to the midlength force has been shown to be small as compared to fiber-fiber interactions. No significant effect of environmental humidity on midlength and end-peak combing forces has been observed. On the other hand, wetting the tress results in a drastic increase in the midlength force and a concurrent decrease in the end-peak force. It appears that surface tension forces involving the liquid film between fibers are largely responsible for this behavior.
Toxin-Antitoxin Modules May Regulate Synthesis of Macromolecules during Nutritional Stress (2000)

The recent enormous expansion of the microbial DNA databases has made it profitable to search for homologues and paralogues (homologues within species) of interesting genes. In combination with genetic, biochemical, and physiological investigations, such analyses may yield new, valuable information
Influence of sampling time on assessment of potential doubling time (1994)

Potential doubling time (Tpot), S-phase transit time (Ts), and labeling index were determined in three experimental rodent tumors by in vivo incorporation of bromodeoxyuridine and flow cytometry. The kinetic parameters were derived from the relative movement method at varying sampling times (time between injection of bromodeoxyuridine and tumor excision). Ts and Tpot were close to the expected (extrapolated) values of the two parameters with sampling time within the range 60-100% of the expected Ts. With short sampling time, Ts and Tpot were considerably over- or underestimated. By use of the original method by (Begg et al., Cytometry 6:620-626, 1985), the Tpot came out with a twofold overestimation with a short sampling time. Generally, modified methods for calculation of Ts did not improve the results. When Tpot is measured in human tumors, there is no a priori knowledge of the kinetic parameters. Consequently, the sampling time must be based on the general experience of tumor cell kinetics in the specific tumor type measured. A relatively long sampling time should be aimed for when measuring Tpot in human tumors. With proper sampling time, Tpot assessed by flow cytometry was found to be a precise and reproducible parameter.
Electric-Field-Assisted Assembly of Perpendicularly Oriented Nanorod Superlattices (2006)

We observe the assembly of CdS nanorod superlattices by the combination of a DC electric field and solvent evaporation. In each electric-field (1 V/microm) assisted assembly, CdS nanorods (5 nm x 30 nm) suspended initially in toluene were observed to align perpendicular to the substrate. Azimuthal alignment along the nanorod crystal faces and the presence of stacking faults indicate that both 2D and 3D assemblies were formed by a process of controlled super crystal growth.
Association between coronary artery calcium score and carotid atherosclerotic disease (2013)

The aim of the present study was to evaluate the association between coronary calcification and carotid atherosclerosis. Briefly, 123 patients with suspected coronary artery disease were recruited. The coronary artery calcium score (CACS) was measured and multi‑contrast carotid magnetic resonance imaging (MRI) was performed. Parameters of the carotid morphological measurements were determined and the presence or absence of carotid plaque tissue compositions was recorded for each subject, as well as plaque surface disruption. Two reviewers blind to CACS status interpreted the MRIs. All the subjects were divided into two groups, high‑ and low‑CACS and the carotid morphological measurements in the CACS groups and categories were compared using independent t‑tests and one way ANOVA, respectively. CACS was found to exhibit a moderate correlation with carotid wall area (WA; r=0.521) and mean wall thickness (MWT; r=0.556) and a weak correlation with total vessel area (TVA; r=0.215) and normalized wall index (r=0.377). No significant correlation between CACS and carotid lumen area was identified. Compared with low‑CACS, the high‑CACS group revealed increased carotid WA, TVA and MWT. In the entire cohort, carotid plaque burden revealed an increasing trend with an increasing CACS. CACS and presence of carotid calcification and lipid‑rich necrotic core (LRNC) demonstrated a significant correlation. No significant correlation was observed between CACS with carotid intraplaque hemorrhage (IPH) and surface disruption. CACS was found to moderately correlate with carotid calcification and LRNC volume and weakly correlate with carotid IPH volume. Results of the present study indicated that CACS significantly correlates with carotid atherosclerotic plaque burden and the presence of tissue compositions.
Hormones and mouse mammary tumorigenesis. (1981)

The hormonal milieu of the host influences viral and chemical carcinogen-induced mammary tumorigenesis in a variety of indirect ways. The effects of a high-fat diet on mouse mammary tumorigenesis are very limited and are convincing only for ice infected by the high-oncogenic mammary tumor virus. The relationship between fat content in the diet, the hormonal milieu of the host, and mammary tumor virus function is unexplored.
A review and perspective: Thin films for optical based chemical sensing at extreme temperatures (2012)

Opportunities exist for energy efficiency improvement and greenhouse gas emission reduction in fossil energy based electrical power generation through deployment of embedded sensors operating at extreme temperatures and under harsh conditions. Despite inherent advantages of optical based sensors, published literature discussing optical sensing materials is limited for temperatures of operation greater than 500°C. A clear need exists for additional fundamental and applied research efforts. Published literature discussing sensor materials for high temperature optical chemical sensing applications are reviewed and research opportunities / needs are highlighted.
Enhanced Generation of Specific Tumor-Reactive CTL In Vitro by Selected Melan-A/MART-1 Immunodominant Peptide Analogues (1998)

The Melan-A/MART-1 gene, which is expressed by normal melanocytes as well as by most fresh melanoma samples and melanoma cell lines, codes for Ags recognized by tumor-reactive CTL. HLA-A*0201-restricted Melan-A-specific CTL recognize primarily the Melan-A(27-35) (AAGIGILTV) and the Melan-A(26-35) (EAAGIGILTV) peptides. The sequences of these two peptides are not necessarily optimal as far as binding to HLA-A*0201 is concerned, since both lack one of the dominant anchor amino acid residues (leucine or methionine) at position 2. In this study we introduced single amino acid substitutions in either one of the two natural peptide sequences with the aim of improving peptide binding to HLA-A*0201 and/or recognition by specific CTL. Surprisingly, analogues of the Melan-A(27-35) peptide, which bound more efficiently than the natural nonapeptide to HLA-A*0201, were poorly recognized by tumor-reactive CTL. In contrast, among the Melan-A(26-35) peptide analogues tested, the peptide ELAGIGILTV was not only able to display stable binding to HLA-A2.1 but was also recognized more efficiently than the natural peptide by two short-term cultured tumor-infiltrated lymph node cell cultures as well as by five of five tumor-reactive CTL clones. Moreover, in vitro generation of tumor-reactive CTL by stimulation of PBMC from HLA-A*0201 melanoma patients with this particular peptide analogue was much more efficient than that observed with either one of the two natural peptides. These results suggest that the Melan-A(26-35) peptide analogue ELAGIGILTV may be more immunogenic than the natural peptides in HLA-A*0201 melanoma patients and should thus be considered as a candidate for future peptide-based vaccine trials.
Recombinant Human Growth/Differentiation Factor 5 Stimulates Mesenchyme Aggregation and Chondrogenesis Responsible for the Skeletal Development of Limbs (1996)

We have expressed and biologically characterized recombinant human growth/differentiation factor 5 (huGDF5). This protein is composed of a mature homodimer consisting of 15 kD subunits. Using recombinant expressed protein, we have demonstrated that huGDF5 in vitro stimulated mesenchyme aggregation and chondrogenesis in rat limb bud cells. In vivo, partially purified huGDF5 induced cartilage and bone formation in muscular tissues of rodents. However, in contrast to the effects of other BMPs, as for example BMP-2, the osteoblastic MC3T3-E1 cells did not respond to huGDF5 as measured by alkaline phosphatase activity. These results suggest that the action of GDF5 may be relatively specific for chondrogenesis during the entire process of the endochondral bone formation. GDF5 may control the morphogenesis of cartilaginous tissue, including joints, in the skeletal development of limbs.
System of systems for autonomous mission decisions (2013)

Manpower is driving up DoD costs while DoD budgets are shrinking; therefore the DoD customer seeks a solution to enable increased mission capacity along with staff reductions. One way to accomplish this is through an autonomous capability to support end-to-end mission activities. The Mission Information Autonomous Intelligent Decision Engine (MiAide) approach for meeting this objective is to create a system of systems (SoS) that work together to enable automation of tasks previously done by humans. MiAide is built upon a novel, but standards-based architecture, that equips MiAide for real end-to-end DoD mission scenarios using a context switching decision engine that distributes actionable information for each specific mission phase to an intelligent mission console (IMC) user interface. The IMC provides secure and high quality communications between mobile end-users and the Mission Operation Center, and it enables graceful handover between operators of different mission phases. MiAide has been demonstrated for aspects of both manned and Unmanned Air Systems (UASs) and proven to reduce staffing while improving mission capacity (e.g., multiply number of missions and mission functions) across all stages of the mission life cycle.
Nanosecond semiconductor diodes for pulsed power switching (2005)

The development of semiconductor-based nano- and subnanosecond high current breakers is crucial for advancing modern research in experimental physics and radioelectronics, particularly with increasing power (to 1010 W) and repetition rate (to 104 Hz) of impulse devices. Highlighted in this review are two types of silicon diodes: drift step recovery diodes (DSRDs) and SOS diodes with the attainable current densities and switched-off powers being 102 A cm−2 and 108 W in the former case, and 105 A cm−2 and 1010 W in the latter. The possibility of utilizing not only monocrystalline silicon (as in DSRDs and SOS diodes) for the base material but also monocrystalline silicon carbide is examined.
Cloning and Characterisation of Two IgE-Binding Proteins, Homologous to Tropomyosin and α-Tubulin, from the Mite <i>Lepidoglyphus destructor</i> (2003)

Two new allergens from L. destructor have been identified and can now be added to the repertoire of recombinant L. destructor allergens. In addition, both these allergens belong to highly conserved protein families and may be important for evaluation of allergenic cross-reactivity.
Tracheal stenosis: An uncommon cause of dyspnea (2010)

A 75-year-old woman presented with worsening dyspnea of about 6 to 8 months' duration. Her symptoms were initially associated with exercise, after about 30 minutes on the treadmill, and now were present at rest. Her breathing pattern had changed to panting to improve airflow during minimal activity.
A shed NKG2D ligand that promotes natural killer cell activation and tumor rejection (2015)

Immune cells, including natural killer (NK) cells, recognize transformed cells and eliminate them in a process termed immunosurveillance. It is thought that tumor cells evade immunosurveillance by shedding membrane ligands that bind to the NKG2D-activating receptor on NK cells and/or T cells, and desensitize these cells. In contrast, we show that in mice, a shed form of MULT1, a high-affinity NKG2D ligand, causes NK cell activation and tumor rejection. Recombinant soluble MULT1 stimulated tumor rejection in mice. Soluble MULT1 functions, at least in part, by competitively reversing a global desensitization of NK cells imposed by engagement of membrane NKG2D ligands on tumor-associated cells, such as myeloid cells. The results overturn conventional wisdom that soluble ligands are always inhibitory and suggest a new approach for cancer immunotherapy.
Threonine 435 of Escherichia coli DnaA Protein Confers Sequence-specific DNA Binding Activity (1997)

The Escherichia coli DnaA protein, as a sequence-specific DNA binding protein, promotes the initiation of chromosomal replication by binding to four asymmetric 9-mer sequences termed DnaA boxes in oriC. Characterization of N-terminal, C-terminal, and internal in-frame deletion mutants identified residues near the C terminus of DnaA protein required for DNA binding. Furthermore, genetic and biochemical characterization of 11 missense mutations mapping within the C-terminal 89 residues indicated that they were defective in DNA binding. Detailed biochemical characterization of one mutant protein bearing a threonine to methionine substitution at position 435 (T435M) revealed that it retained only nonspecific DNA binding activity, suggesting that threonine 435 imparts specificity in binding. Finally, T435M was inactive on its own for in vitro replication of an oriC plasmid but was able to augment limiting levels of wild type DnaA protein, consistent with the proposal that not all of the DnaA monomers in the initial complex are bound specifically to oriC and that direct interaction occurs among monomers.
Dietary Fucoxanthin Increases Metabolic Rate and Upregulated mRNA Expressions of the PGC-1alpha Network, Mitochondrial Biogenesis and Fusion Genes in White Adipose Tissues of Mice (2014)

The mechanism for how fucoxanthin (FX) suppressed adipose accumulation is unclear. We aim to investigate the effects of FX on metabolic rate and expressions of genes related to thermogenesis, mitochondria biogenesis and homeostasis. Using a 2 × 2 factorial design, four groups of mice were respectively fed a high sucrose (50% sucrose) or a high-fat diet (23% butter + 7% soybean oil) supplemented with or without 0.2% FX. FX significantly increased oxygen consumption and carbon dioxide production and reduced white adipose tissue (WAT) mass. The mRNA expressions of peroxisome proliferator-activated receptor (PPAR) γ coactivator-1α (PGC-1α), cell death-inducing DFFA-like effecter a (CIDEA), PPARα, PPARγ, estrogen-related receptor α (ERRα), β3-adrenergic receptor (β3-AR) and deiodinase 2 (Dio2) were significantly upregulated in inguinal WAT (iWAT) and epididymal WAT (eWAT) by FX. Mitochondrial biogenic genes, nuclear respiratory factor 1 (NRF1) and NRF2, were increased in eWAT by FX. Noticeably, FX upregulated genes of mitochondrial fusion, mitofusin 1 (Mfn1), Mfn2 and optic atrophy 1 (OPA1), but not mitochondrial fission, Fission 1, in both iWAT and eWAT. In conclusion, dietary FX enhanced the metabolic rate and lowered adipose mass irrespective of the diet. These were associated with upregulated genes of the PGC-1α network and mitochondrial fusion in eWAT and iWAT.
Multi-organ automatic segmentation in 4D contrast-enhanced abdominal CT (2008)

Medical imaging and computer-aided diagnosis (CAD) traditionally focus on organ- or disease-based applications. To shift from organ-based to organism-based approaches, CAD needs to replicate the work of radiologists and analyze consecutively multiple organs. A fully automatic method is presented for the simultaneous segmentation of four abdominal organs from 4D CT data. Abdominal contrast- enhanced CT scans from sixteen patients were obtained at three phases: non-contrast, arterial and portal. Intra- patient data is registered non-rigidly using the demons algorithm and smoothed with anisotropic diffusion. Mutual information accounts for intensity variability within the same organ during subsequent acquisitions and data are interpolated with cubic B-splines. Then heterogeneous erosion is applied to multi-phase data using the intensity characteristics of the liver, spleen, and kidneys. The erosion filter is a 4D convolution that preserves only image regions that satisfy the above intensity criteria. Finally, a geodesic level set completes the segmentation of the four abdominal organs. This 3D evaluation of abdominal data shows great promise as a computer-aided radiology tool for multi-organ and multi-disease analysis.
Stem Cell Review Series: Aging of the skeletal muscle stem cell niche (2008)

Declining stem cell function during aging contributes to impaired tissue function. Muscle-specific stem cells ('satellite cells') are responsible for generating new muscle in response to injury in the adult. However, aged muscle displays a significant reduction in regenerative abilities and an increased susceptibility to age-related pathologies. This review describes components of the satellite cell niche and addresses how age-related changes in these components impinge on satellite cell function. In particular, we review changes in the key niche elements, the myofiber and the basal lamina that are in intimate contact with satellite cells. We address how these elements are influenced by factors secreted by interstitial cells, cells of the immune system, and cells associated with the vasculature, all of which change with age. In addition, we consider more distant sources of influence on the satellite cell niche that change with age, such as neural-mediated trophic factors and electrical activity and systemic factors present in the circulation. A better understanding of the niche elements and their influence on the satellite cell will facilitate the development of therapeutic interventions aimed at improving satellite cell activity and ultimately tissue response to injury in aged individuals.
Functionalized Higher Acenes:  Hexacene and Heptacene (2005)

We have extended our functionalization strategy for pentacene to the higher acenes hexacene and heptacene. Provided a large enough alkyne substituent is used, these large aromatic rods are both stable and soluble and can be characterized spectroscopically as well as by single-crystal X-ray diffraction.
Mutational studies of human DNA polymerase alpha. Serine 867 in the second most conserved region among alpha-like DNA polymerases is involved in primer binding and mispair primer extension. (1993)

The second most conserved region of alpha-like DNA polymerases, region II, spans a block of 40 amino acid residues centered at the core sequence -DFNSLYPSII-. In the previous paper, we described mutational studies of 3 amino acid residues in region II which includes 2 amino acid residues in the core sequence. We showed that residues Asp860 and Tyr865 in the core sequence are involved in substrate deoxynucleotide triphosphate (dNTP) binding. We further showed that the phenyl moiety of the Tyr865 side chain interacts with the incoming dNTP and is responsible for the misinsertion fidelity of the enzyme. In this report, we investigated the function of 2 serine residues, Ser863 and Ser867, in this core sequence. Mutation of these 2 Ser residues to either Ala or Thr yielded mutant enzymes with similar Km for dNTPs, kcat, processivity, and misinsertion fidelity of DNA synthesis as the wild type enzyme. However, mutation of Ser867 to Ala demonstrated a 30-fold increase in Km for primer-template and a 5-fold higher KD for binding primer-template. DNA footprinting experiments of primer with the dideoxynucleotide terminus indicated that the structural feature of the primer recognized by Ser867 is the 3'-OH terminus. Single-stranded DNA inhibition data suggest that removal of the hydroxyl side chain of Ser867 affects the polymerase's interaction with primer and not with template. Mutation of Ser867 to Ala also decreases the mutant enzyme's Km for dNTP to extend a mispaired primer and thus enhances its capacity to extend a mispaired primer terminus. These data support the conclusion that the hydroxyl side chain of Ser867 of human DNA polymerase alpha is involved in primer interaction during DNA synthesis and plays an essential role in mispair extension fidelity of DNA synthesis.