gebhart/patrepeval huggingface dataset:
van der Waals Metallic Transition Metal Dichalcogenides (2018)

Transition metal dichalcogenides are layered materials which are composed of transition metals and chalcogens of the group VIA in a 1:2 ratio. These layered materials have been extensively investigated over synthesis and optical and electrical properties for several decades. It can be insulators, semiconductors, or metals revealing all types of condensed matter properties from a magnetic lattice distorted to superconducting characteristics. Some of these also feature the topological manner. Instead of covering the semiconducting properties of transition metal dichalcogenides, which have been extensively revisited and reviewed elsewhere, here we present the structures of metallic transition metal dichalcogenides and their synthetic approaches for not only high-quality wafer-scale samples using conventional methods (e.g., chemical vapor transport, chemical vapor deposition) but also local small areas by a modification of the materials using Li intercalation, electron beam irradiation, light illumination, pressures, and strains. Some representative band structures of metallic transition metal dichalcogenides and their strong layer-dependence are reviewed and updated, both in theoretical calculations and experiments. In addition, we discuss the physical properties of metallic transition metal dichalcogenides such as periodic lattice distortion, magnetoresistance, superconductivity, topological insulator, and Weyl semimetal. Approaches to overcome current challenges related to these materials are also proposed.
Immunophilins: structure—function relationship and possible role in microbial pathogenicity (1993)

Immunophilins are housekeeping proteins present in a wide variety of organisms. Members of two protein superfamilies, cyclophilins (Cyps) and FK506-binding proteins (FKBPs) belong to this class of immunophilins. Despite the fact that the amino acid sequences of Cyp and FKBPs do not exhibit noticeable homology to each other, proteins of both classes are able to ligate immunosuppressive peptide derivatives. Cyps form complexes with the cyclic undercapeptide cyclosporin A and FKBPs are able to bind FK506 as well as rapamycin, both of which have a pipecolyl bond within their structure. In a ligand-bound form, immunophilins interfere with signal transduction in T cells. In addition, immunophilins have peptidyl prolyl cis-trans isomerase (PPlase) activity and are able to accelerate the rate of conformational events in proline-containing polypeptides. Microorganisms produce proteins that exhibit extensive sequence homologies to cyclophilins and FKBPs of higher organisms and which have considerable PPlase catalytic activity. While cyclophilins seem to be present in most if not all microbial species investigated, FKBPs are produced by yeasts as well as by a number of pathogenic bacteria, such as Legionella pneumophila, Chlamydia trachomatis and Neisseria meningitidis. The Mip protein of L. pneumophila is a virulence factor that plays an essential role in the ability of the bacteria to survive and multiply in phagocytic cells. Some results are summarized on the structure and putative functions of immunophilins and place special emphasis on the contribution of these polypeptides to the virulence of pathogenic microorganisms.
SD-VBS: The San Diego Vision Benchmark Suite (2009)

In the era of multi-core, computer vision has emerged as an exciting application area which promises to continue to drive the demand for both more powerful and more energy efficient processors. Although there is still a long way to go, vision has matured significantly over the last few decades, and the list of applications that are useful to end users continues to grow. The parallelism inherent in vision applications makes them a promising workload for multi-core and many-core processors. While the vision community has focused many years on improving the accuracy of vision algorithms, a major barrier to the study of their computational properties has been the lack of a benchmark suite that simultaneously spans a wide portion of the vision space and is accessible in a portable form that the architecture community can easily use. We present the San Diego Vision Benchmark Suite (SD-VBS), a suite of diverse vision applications drawn from the vision domain. The applications are drawn from the current state-of-the-art in computer vision, in consultation with vision researchers. Each benchmark is provided in both MATLAB and C form. MATLAB is the preferred language of vision researchers, while C makes it easier to map the applications to research platforms. The C code minimizes pointer usage and employs clean constructs to make them easier for parallelization. Furthermore, we provide a spectrum of input sets that enable researchers to control simulation time, and to understand properties as inputs increase to leverage better processor performance. In this paper, we describe the benchmarks, show how their runtime is attributed to their constituent kernels, overview some of their computational properties - including parallelism - and show how they are affected by growing inputs. The benchmark suite will be made available on the Internet, and updated as new applications emerge.
Induction of virus-neutralizing antibodies by bacteria expressing the C3 poliovirus epitope in the periplasm. The route of immunization influences the isotypic distribution and the biologic activity of the antipoliovirus antibodies. (1990)

Abstract Two viral epitopes (C3 neutralization epitope from poliovirus type 1 and the 132-145 peptide from the PreS2 region from hepatitis B virus) have been expressed in the Escherichia coli periplasm as protein fusion with the maltose binding protein (MalE protein). Immunization of mice with live bacteria expressing the foreign viral epitopes in their periplasm elicited high antibody titers against the viral peptide as well as against the corresponding virus. This demonstrates for the first time in the case of defined epitopes that, when live bacteria are used as immunogens, presentation at the cell surface is not a prerequisite to obtain an antibody response. On the other hand, the induction of antiviral antibody responses by these recombinant bacteria depended dramatically on the route of immunization: a response was induced by live bacteria through the i.v. route but not through the s.c. route. However, when bacteria were heat killed or when the MalE hybrid protein was released under a soluble form from the cell, a response was induced even upon s.c. immunization. From these results, we suggest that in order to induce high levels of antibodies by the s.c. route, a major parameter for bacterial Ag would be their capacity to be released into a soluble form before the interaction of the bacteria with the APC. This would permit the presentation by B cells rather than by phagocytic cells. Finally, we demonstrate that the route of immunization influences the isotypic distribution and the neutralizing activity of the antipoliovirus antibodies. Such results may have major implications for the development of bacterial vaccines based on fusion proteins.
Electrical activity at the sympathetic neuroeffector junction in the guinea‐pig vas deferens. (1988)

1. The relationship between the nerve terminal action potential and transmitter release from sympathetic postganglionic nerve terminals has been studied in vitro by focal extracellular recording. 2. In the absence of stimulation, 'spontaneous excitatory junction currents' (SEJCs) were recorded with amplitudes up to 500 microV, durations of 50‐80 ms and frequencies of occurrence of 0.3‐0.05 Hz; SEJCs of unusually long time course were also observed. The SEJCs were not recorded in tissues pre‐treated with 6‐hydroxydopamine to destroy sympathetic nerves, were unaffected by tetrodotoxin (TTX), the competitive alpha‐adrenoceptor antagonists, prazosin and phentolamine, the irreversible alpha‐adrenoceptor antagonist benextramine but were blocked by alpha,beta‐methylene ATP which desensitizes P2‐purinoceptors. 3. During trains of supramaximal stimuli at 0.1‐4 Hz stimulus locked 'excitatory junction currents' (EJCs) were evoked intermittently from the population of varicosities located under the suction electrode with a probability of occurrence of 0.005‐0.8. Although EJCs occurred intermittently, they were always preceded by an associated, non‐intermittent, nerve impulse (delay less than or equal to 3 ms). 4. The EJCs reflect transmitter release from nerves because they were abolished by TTX, removal of calcium from the bathing medium, exposure to alpha‐beta‐methylene ATP and exhibited frequency‐dependent facilitation. 5. Amplitude distributions of SEJCs and EJCs recorded in the same attachment were similar and skewed towards low‐amplitude events. Individual SEJCs and EJCs could be found which were identical in amplitude and time course. 6. Locally applied TTX blocked impulse propagation and transmitter release in the terminal region; electrotonic invasion of the terminals from the point of block did not activate the transmitter release process. 7. These studies indicate that (1) intermittence of transmitter release is caused by a low probability of release in the invaded varicosity and is not caused by conduction failure in the terminal regions, (2) only a single quantum is normally secreted when the release mechanism of a varicosity is activated by the nerve impulse and (3) active invasion of the terminals is necessary for transmitter release to occur.
How do changes in the mtDNA and mitochondrial dysfunction influence cancer and cancer therapy? Challenges, opportunities and models (2015)

Several mutations in nuclear genes encoding for mitochondrial components have been associated with an increased cancer risk or are even causative, e.g. succinate dehydrogenase (SDHB, SDHC and SDHD genes) and iso-citrate dehydrogenase (IDH1 and IDH2 genes). Recently, studies have suggested an eminent role for mitochondrial DNA (mtDNA) mutations in the development of a wide variety of cancers. Various studies associated mtDNA abnormalities, including mutations, deletions, inversions and copy number alterations, with mitochondrial dysfunction. This might, explain the hampered cellular bioenergetics in many cancer cell types. Germline (e.g. m.10398A>G; m.6253T>C) and somatic mtDNA mutations as well as differences in mtDNA copy number seem to be associated with cancer risk. It seems that mtDNA can contribute as driver or as complementary gene mutation according to the multiple-hit model. This can enhance the mutagenic/clonogenic potential of the cell as observed for m.8993T>G or influences the metastatic potential in later stages of cancer progression. Alternatively, other mtDNA variations will be innocent passenger mutations in a tumor and therefore do not contribute to the tumorigenic or metastatic potential. In this review, we discuss how reported mtDNA variations interfere with cancer treatment and what implications this has on current successful pharmaceutical interventions. Mutations in MT-ND4 and mtDNA depletion have been reported to be involved in cisplatin resistance. Pharmaceutical impairment of OXPHOS by metformin can increase the efficiency of radiotherapy. To study mitochondrial dysfunction in cancer, different cellular models (like ρ(0) cells or cybrids), in vivo murine models (xenografts and specific mtDNA mouse models in combination with a spontaneous cancer mouse model) and small animal models (e.g. Danio rerio) could be potentially interesting to use. For future research, we foresee that unraveling mtDNA variations can contribute to personalized therapy for specific cancer types and improve the outcome of the disease.
An update of Coenzyme Q10 implications in male infertility: Biochemical and therapeutic aspects (2005)

This review is focused upon the role of coenzyme Q(10) in male infertility in the light of a broader issue of oxidative damage and antioxidant defence in sperm cells and seminal plasma. Reactive oxygen species play a key pathogenetic role in male infertility besides having a well-recognized physiological function. The deep involvement of coenzyme Q(10) in mitochondrial bioenergetics and its antioxidant properties are at the basis of its role in seminal fluid. Following the early studies addressing its presence in sperm cells and seminal plasma, the relative distribution of the quinone between these two compartments was studied in infertile men, with special attention to varicocele. The reduction state of CoQ(10) in seminal fluid was also investigated. After the first in vitro experiments CoQ(10) was administered to a group of idiopathic asthenozoospermic infertile patients. Seminal analysis showed a significant increase of CoQ(10) both in seminal plasma and in sperm cells, together with an improvement in sperm motility. The increased concentration of CoQ(10) in seminal plasma and sperm cells, the improvement of semen kinetic features after treatment, and the evidence of a direct correlation between CoQ(10) concentrations and sperm motility strongly support a cause/effect relationship. From a general point of view, a deeper knowledge of these molecular mechanisms could lead to a new insight into the so-called unexplained infertility.
Characterization of Ig Gene Somatic Hypermutation in the Absence of Activation-Induced Cytidine Deaminase (2008)

Somatic hypermutation (SHM) of Ig genes depends upon the deamination of C nucleotides in WRCY (W = A/T, R = A/G, Y = C/T) motifs by activation-induced cytidine deaminase (AICDA). Despite this, a large number of mutations occur in WA motifs that can be accounted for by the activity of polymerase eta (POL eta). To determine whether there are AICDA-independent mutations and to characterize the relationship between AICDA- and POL eta-mediated mutations, 1470 H chain and 1313 kappa- and lambda-chain rearrangements from three AICDA(-/-) patients were analyzed. The Ig mutation frequency of all V(H) genes from AICDA(-/-) patients was 40-fold less than that of normal donors, whereas the mutation frequency of mutated V(H) sequences from AICDA(-/-) patients was 6.8-fold less than that of normal donors. AICDA(-/-) B cells lack mutations in WRCY/RGYW motifs as well as replacement mutations and mutational targeting in complementarity-determining regions. A significantly reduced mutation frequency in WA motifs compared with normal donors and an increased percentage of transitions, which may relate to reduced uracil DNA-glycosylase activity, suggest a role for AICDA in regulating POL eta and uracil DNA-glycosylase activity. Similar results were observed in V(L) rearrangements. The residual mutations were predominantly G:C substitutions, indicating that AICDA-independent cytidine deamination was a likely, yet inefficient, mechanism for mutating Ig genes.
Upper extremity central venous obstruction in hemodialysis patients: treatment with Wallstents. (1997)

After suboptimal angioplasty, treatment of subclavian and brachiocephalic vein stenoses with a Wallstent can provide continued use of a hemodialysis access. Close clinical surveillance and multiple reinterventions are necessary to maintain Wallstent patency.
Maturation‐dependent repair of untreated osteochondral defects in the rabbit knee joint (1997)

Repair of untreated full-thickness cartilage defects in the medial femoral knee condyle was studied in 17 young, 21 adolescent, and 19 adult rabbits. At 6 weeks, the defect was completely filled by tissue regeneration in all young and adolescent animals, but in only few of the adults (p < 0.05). The morphology of all repairs improved from fibrous tissue to hyaline-like cartilage over time (p < 0.05), but at 3 and 6 weeks, the repair tissue in young and adolescent rabbits was more cartilage-like than in the adults (p < 0.05). In addition, bonding of the repair tissue to the adjacent cartilage was better in the young and adolescent than in the adult animals (p < 0.05). At 12 weeks, subchondral bone had formed in some young and adolescent repairs, but in no case in the adults. None of the repairs showed normal cartilage appearance, but formation of hyaline-like cartilage was common at 12 weeks. Irrespective of age or observation time, the repair site showed decreased stiffness and larger strain values compared to adjacent or control cartilage (p < 0.001) with no tendency for improvement over time. Younger animals showed a faster filling of the defect and an earlier specialization of the repair tissue than adult animals, but the mechanical quality of the regenerated tissue remained inferior to normal. © 1997 John Wiley & Sons, Inc.
Analysis of folylpoly-γ-glutamate synthetase gene expression in human B-precursor ALL and T-lineage ALL cells (2006)

We demonstrated that the minimal FPGS promoter region previously described in CCRF-CEM is not sufficient to effectively drive FPGS transcription in NALM6 cells, suggesting that different regulatory elements are required for FPGS gene expression in Bp-cells. Our data indicate that the control of FPGS expression in human hematopoietic cells is complex and involves lineage-specific differences in regulatory elements, transcription initiation rates, and mRNA processing. Understanding the lineage-specific mechanisms of FPGS expression should lead to improved therapeutic strategies aimed at overcoming MTX resistance or inducing apoptosis in leukemic cells.
Bone marrow–derived stem cells preserve cone vision in retinitis pigmentosa (2004)

Retinitis pigmentosa is a heritable group of blinding diseases resulting from loss of photoreceptors, primarily rods and secondarily cones, that mediate central vision. Loss of retinal vasculature is a presumed metabolic consequence of photoreceptor degeneration. A new study shows that autologous bone marrow-derived lineage-negative hematopoietic stem cells, which incorporate into the degenerating blood vessels in two murine models of retinitis pigmentosa, rd1 and rd10, prevent cone loss. The use of autologous bone marrow might avoid problems with rejection while preserving central cone vision in a wide variety of genetically disparate retinal degenerative diseases.
Incidence of and Treatment for Ductal Carcinoma In Situ of the Breast (1996)

Incidence rates of DCIS of the breast have increased dramatically since 1983. This increase correlates with the widespread adoption of modern mammographic screening. While early detection of invasive breast cancer is beneficial, the value of DCIS detection is currently unknown. There is cause for concern about the large number of DCIS cases that are being diagnosed as a consequence of screening mammography, most of which are treated by some form of surgery. In addition, the proportion of cases treated by mastectomy may be inappropriately high, particularly in some areas of the United States.
Increased PTHRP production by a tyrosine kinase oncogene, Tpr-Met: role of the Ras signaling pathway (1996)

We have used the Tpr-Met oncogene as a model to examine signaling pathways of growth factors and tyrosine kinase oncogenes that can increase parathyroid hormone-related peptide (PTHRP) production. PTHRP production in Tpr-Met transfected cells, when assessed by Northern blot analysis and radioimmunoassay, was increased four- to eightfold. Treatment of these cells with the transcriptional inhibitor actinomycin D and nuclear run-off assays showed that the major cause of increased PTHRP mRNA was enhanced gene transcription. To analyze the intracellular signaling molecules involved in PTHRP production, stable cell lines expressing a Tyr489 Phe mutant of the Tpr-Met oncoprotein were examined. The mutant fails to activate phosphatidylinositol (PI)-3 kinase or associate with the Grb-2 adaptor protein and caused a significant reduction in PTHRP production. Treatment of wild-type Tpr-Met transfected cells with wortmannin, a PI-3 kinase inhibitor, had no effect on PTHRP production; however, treatment of these cells with lovastatin, an inhibitor of p21ran isoprenylation, significantly reduced PTHRP expression. These results show that PTHRP is a downsteam target of the Tpr-Met oncogene and indicate that the PTHRP stimulating activity is mediated via the Ras signaling pathway.
Prediction of human rotavirus serotype by nucleotide sequence analysis of the VP7 protein gene (1988)

Human rotavirus field isolates were characterized by direct sequence analysis of the gene encoding the serotype-specific major neutralization protein (VP7). Single-stranded RNA transcripts were prepared from virus particles obtained directly from stool specimens or after two or three passages in MA-104 cells. Two regions of the gene (nucleotides 307 through 351 and 670 through 711) which had previously been shown to contain regions of sequence divergence among rotavirus serotypes were sequenced by the dideoxynucleotide method with two different synthetic oligonucleotide primers. The resulting nucleotide sequences were compared with the corresponding sequences from rotaviruses of known serotype (serotype 1, 2, 3, or 4). A total of 25 field isolates and 10 laboratory strains examined by this method exhibited marked sequence identity in both areas of the gene with the corresponding regions of 1 of the 4 reference strains. In addition, the predicted serotype from the sequence analysis correlated in each case with the serotype determined when the rotaviruses were examined by plaque reduction neutralization or reactivity with serotype-specific monoclonal antibodies. These data suggest that as a result of the high degree of sequence conservation observed among rotaviruses of the same serotype, it is possible to predict the serotype of a rotavirus isolate by direct sequence analysis of its VP7 gene.
Physical chemistry of inorganic polymeric and composite materials (1992)

Composite (heterophase) materials crystal structure of inorganic compounds nature of phases of composite materials interphase interactions and investigation methods of solid state polymer glass-like and metallic materials composite coatings deposited from electrolytes and suspensions untraditional states of substance and methods for their modifications.
Tracking and modeling focus of attention in meetings. (2002)

Anaerobic digestion (AD) has been used for wastewater treatment and production of renewable energy or biogas. Propionate accumulation is one of the important problems leading to an unstable system and low methane production. Revealing propionate-degrading microbiome is necessary to gain a better knowledge for alleviation of the problem. Herein, we systematically investigated the propionate-degrading cultures enriched from various anaerobic sludge sources of agro-industrial wastewater treatment plants using 16S rRNA gene sequencing. Different microbial profiles were shown even though the methanogenic activities of all cultures were similar. Interestingly, non-classical propionate-degrading key players <i>Smithella</i>, <i>Syntrophomonas,</i> and <i>Methanosaeta</i> were observed as common prevalent taxa in our enriched cultures. Moreover, different hydrogenotrophic methanogens were found specifically to the different sludge sources. The enriched culture of high salinity sludge showed a distinct microbial profile compared to the others, containing mainly <i>Thermovirga</i>, <i>Anaerolinaceae</i>, <i>Methanosaeta</i>, <i>Syntrophobactor,</i> and <i>Methanospirillum</i>. Our microbiome analysis revealed different propionate-degrading community profiles via mainly the <i>Smithella</i> pathway and offers inside information for microbiome manipulation in AD systems to increase biogas production corresponding to their specific microbial communities.
Insulated-gate and junction-gate FET's of CVD-Grown β-SiC (1987)

An insulated-gate field effect transistor (IGFET) and a junction-gate FET (JFET) of cubic silicon carbide (β-SiC) have been fabricated using chemical vapor deposition (CVD) growth on Si substrate. In order to improve the characteristics, a boron-doped p-layer is used under the n-channel layer. Both FET's show clear drain characteristics for the first time using CVD-grown β-SiC.