gebhart/patrepeval huggingface dataset:
Toward a comprehensive view of cancer immune responsiveness: a synopsis from the SITC workshop (2019)

Tumor immunology has changed the landscape of cancer treatment. Yet, not all patients benefit as cancer immune responsiveness (CIR) remains a limitation in a considerable proportion of cases. The multifactorial determinants of CIR include the genetic makeup of the patient, the genomic instability central to cancer development, the evolutionary emergence of cancer phenotypes under the influence of immune editing, and external modifiers such as demographics, environment, treatment potency, co-morbidities and cancer-independent alterations including immune homeostasis and polymorphisms in the major and minor histocompatibility molecules, cytokines, and chemokines. Based on the premise that cancer is fundamentally a disorder of the genes arising within a cell biologic process, whose deviations from normality determine the rules of engagement with the host's response, the Society for Immunotherapy of Cancer (SITC) convened a task force of experts from various disciplines including, immunology, oncology, biophysics, structural biology, molecular and cellular biology, genetics, and bioinformatics to address the complexity of CIR from a holistic view. The task force was launched by a workshop held in San Francisco on May 14-15, 2018 aimed at two preeminent goals: 1) to identify the fundamental questions related to CIR and 2) to create an interactive community of experts that could guide scientific and research priorities by forming a logical progression supported by multiple perspectives to uncover mechanisms of CIR. This workshop was a first step toward a second meeting where the focus would be to address the actionability of some of the questions identified by working groups. In this event, five working groups aimed at defining a path to test hypotheses according to their relevance to human cancer and identifying experimental models closest to human biology, which include: 1) Germline-Genetic, 2) Somatic-Genetic and 3) Genomic-Transcriptional contributions to CIR, 4) Determinant(s) of Immunogenic Cell Death that modulate CIR, and 5) Experimental Models that best represent CIR and its conversion to an immune responsive state. This manuscript summarizes the contributions from each group and should be considered as a first milestone in the path toward a more contemporary understanding of CIR. We appreciate that this effort is far from comprehensive and that other relevant aspects related to CIR such as the microbiome, the individual's recombined T cell and B cell receptors, and the metabolic status of cancer and immune cells were not fully included. These and other important factors will be included in future activities of the taskforce. The taskforce will focus on prioritization and specific actionable approach to answer the identified questions and implementing the collaborations in the follow-up workshop, which will be held in Houston on September 4-5, 2019.
Once‐Daily Aminoglycoside in the Treatment of Enterococcus faecalis Endocarditis: Case Report and Review (2000)

Once-daily administration of aminoglycosides (ODA) is effective and safe for many indications. By optimizing pharmacodynamic principles, it enhances bactericidal activity and minimizes toxicity. Its use for the treatment of enterococcal infection is controversial, however, and results of in vitro studies and animal models of endocarditis are conflicting. To date, no case reports or clinical trials have examined its utility in human enterococcal endocarditis. A patient with right-sided endocarditis caused by Enterococcus faecalis was managed by once-daily gentamicin. Clinical and bacteriologic cures of this patient raise questions as to whether enterococcal endocarditis should be regarded as contraindication to ODA. The clinical utility of ODA in this disease deserves further investigation.
P‐glycoprotein is expressed and causes resistance to chemotherapy inEBV‐positive T‐cell lymphoproliferative diseases (2015)

Epstein-Barr virus-positive T-cell lymphoproliferative diseases (EBV-T-LPDs) are rare lymphomas with poor prognosis. Although chemotherapeutic strategies such as CHOP have been often selected, they have exhibited only limited efficacy. To clarify the mechanism of chemoresistance, we examined P-glycoprotein (P-gp) expression. P-gp acts as an energy-dependent efflux pump that excretes drugs from the cytoplasm, resulting in low-intracellular drug concentrations and poor sensitivity to chemotherapy. We examined P-gp expression in EBV-positive cells by immunohistochemistry staining in three patients of EBV-T-LPDs and the expression was detected in all patients. We also examined mdr1 mRNA expression by reverse-transcriptase polymerase-chain reaction (RT-PCR) in EBV-positive tumor cells from these patients and additional three patients. The expression was detected in all examined patients. In five EBV-T-LPDs patients, P-gp function was detected by Rhodamine-123 efflux assay in these cells. The efflux was inhibited by treatment with a P-gp inhibitor, cyclosporine A (CsA). We also examined and detected P-gp expression in EBV-positive T-cell lines SNT8 and SNT16 established from EBV-T-LPDs patients, by RT-PCR and western blotting. The function was also detected by Rhodamine-123 efflux in these cell lines. Inhibition and knock down of P-gp by CsA and siRNA, respectively, enhanced etoposide- and doxorubicin-induced cell death in the EBV-positive T-cell lines. Finally, we infected the T-cell line MOLT4 with EBV, and found that mdr1 mRNA expression and Rhodamine 123 efflux were upregulated after infection. These results indicated that enhanced P-gp expression contributed to the chemoresistance of EBV-T-LPDs.
Dissection of the ribonuclease T1 subsite (1992)

Ribonuclease T1 contains a subsite which by interacting with the leaving nucleoside N of GpN dinucleoside phosphate substrates, contributes to catalysis [Steyaert, J., Wyns, L. & Stanssens, P. (1991) Biochemistry 30, 8661-8665]. The Asn36Ala and Asn98Ala mutations reduce the transesterification rates of GpA, GpC and GpU considerably whereas they have virtually no effect on the transesterification kinetics of the synthetic substrate guanosine 3'-(methyl phosphate) (GpMe) (in which the leaving nucleoside is replaced by methanol), indicating that the Asn36 and Asn98 side chains are part of the RNase T1 subsite [Steyaert, J., Haikal, A. F., Wyns, L. & Stanssens, P. (1991) Biochemistry 30, 8666-8670]. The kinetics of the Asn36Ala, Asn98Ala and wild-type catalyzed transesterification of guanosine 3'-(5'-D-ribosyl phosphate) (GpRib), another GpN analog in which the leaving groups is replaced by D-ribose, enables the mapping of the subsite interactions provided by Asn36 and Asn98. We find that the Asn36 amide function contributes 4.6 kJ/mol to catalysis through interactions with the ribose moiety of the leaving nucleoside. Asn98 is at least in part responsible for the subsite preference for cytidine; the Asn98 side chain preferentially binds cytosine as the leaving nucleoside base.
<title>Improved method for measuring low-level linear birefringence in optical materials</title> (1998)

The authors reports in this paper a sensitive method for measuring low-level linear birefringence in optical materials. A photoelastic modulator is employed as the polarization modulation device in the set-up. The sensitivity of this method is evaluated to be at approximately 0.003 nm (approximately 0.002 degree(s) at 632.8 nm) by measuring the mechanically induced linear birefringence in a fused silica optical element. The capability of this method is demonstrated by determining the residual linear birefringence below 0.1 nm in several high quality optical elements.
Tunable diode laser spectroscopy for gas detection inside scattering media (2006)

The present communication is mainly focused on molecular oxygen detection in porous organic matter, through a tunable diode laser spectroscopy. Initial measurements on wood were preformed in order to illustrate the influence of the density and anisotropy of the sample on the GASMAS-signal. Additional measurements were performed on horticultural produces, in which the concentration of the molecular oxygen gas is of crucial importance for the ripening process and the quality of the produces. The methodology presented is general and can be applied to a large number of problems concerning gas exchange in porous materials, which can be of interest in applications ranging from biological and medical to industrial and pharmaceutical
Transplantation of bone marrow-derived mesenchymal stem cells rescues partially rachitic phenotypes induced by 1,25-Dihydroxyvitamin D deficiency in mice. (2016)

To determine whether the transplantation of bone marrow-derived mesenchymal stem cells (BM-MSCs) can improve the 1,25(OH)<sub>2</sub>D deficiency-induced rachitic phenotype, 2×10<sup>6</sup> BM-MSCs from wild-type mice or vehicle were transplanted by tail vein injection into mice deficient in 1,25(OH)<sub>2</sub>D due to targeted deletion of 1α(OH)ase (1α(OH)ase<sup>-/-</sup>). Our results show that 1α(OH)ase mRNA was expressed in the BM-MSCs derived from wild-type mice, and was detected in long bone, kidney and intestine from BM-MSC-transplanted 1α(OH)ase<sup>-/-</sup> recipients. Serum calcium, 1,25(OH)<sub>2</sub>D<sub>3</sub> levels and body weight were significantly increased in BM-MSC-transplanted 1α(OH)ase<sup>-/-</sup> recipients compared to vehicle-treated 1α(OH)ase<sup>-/-</sup> mice. Skeletal mineralization improved in 1α(OH)ase<sup>-/-</sup> recipients as demonstrated by BMD measurement, micro-CT analysis and von Kossa staining of undecalcified sections. Expression levels of type I collagen, osteocalcin, bone sialoprotein and vitronectin and the size of calcified nodules were decreased in BM-MSC cultures from 1α(OH)ase<sup>-/-</sup> mice compared with those from wild-type mice, however, these parameters were increased in those from BM-MSCs-transplanted 1α(OH)ase<sup>-/-</sup> recipients compared with those from vehicle-treated 1α(OH)ase<sup>-/-</sup> mice. This study indicates that donor BM-MSCs cells can relocate to multiple tissues where they synthesize 1α(OH)ase and produce 1,25(OH)<sub>2</sub>D that contributes to the improvement of serum calcium and skeletal mineralization. Results from this study suggest that BM-MSC transplantation may provide a therapeutic approach to treatment of pseudovitamin D-deficiency rickets.
Contact modelling by the finite element method : Application to the piezoelectric motor (1999)

The operating principle of the piezoelectric motor is based upon various physical phenomena, among which one could mention the acoustic vibration and the friction between the stator and the rotor. In tour laboratory a finite element code called ATILA has been developed. ATILA is efficient to perform static, modal or harmonic analysises for elastic structures. During the last two decades, the contact modeling drew the attention of numerous research groups. suggesting numerical approach by the finite element. However, most of these numerical studies require heavy programming techniques. In this paper we suggest an algorithm in order to treat the problem of contact with or without friction. This algorithm is based on a technique of mathematical simple programming using the method of static condensations Finally, an application to the piezoelectric motor is presented. The present study focused on the intcrfhce between the stator and the rotor, where the acoustic energy is converted into the spinning of the rotor through the friction mechanism. The contact algorithm presented in this paper allows the contact surface, the normal and tangential stresses to be determined as a function of the interface parameters. The results are validated by comparing will piezoelectric motor experimental data.
A lane marking extraction approach based on Random Finite Set Statistics (2013)

Within the past few years, lane detection technology has become of high interest in the field of intelligent vehicles; however, robustness is still an issue. The challenge is to extract the lane markings effectively from the complex urban environment. In this paper, we present a novel approach based on Random Finite Set Statistics for estimating the position of lane markings. We rely on Probability Hypothesis Density (PHD) filtering and apply this technique to lane marking extraction in urban environment. Our method is based on two phases: an image preprocessing phase to extract pixels that potentially represent lanes and a tracking phase to identify lane markings. Compared to other approaches, our method presents a recursive filtering algorithm which extracts lane markings in the presence of clutter and non-lane markings. The experimental results exhibit the high performance of the proposed approach under various scenarios.
Evidence for Association of Polycystic Ovary Syndrome in Caucasian Women with a Marker at the Insulin Receptor Gene Locus (2001)

The polycystic ovary syndrome (PCOS) is one of the commonest female endocrinopathies affecting 5-10% of women of reproductive age. The disorder, characterized by chronic anovulation and signs of hyperandrogenism, results from a complex interaction between genetic predisposing factors and environmental triggers. We have studied 85 Caucasian PCOS patients and 87 age-matched Caucasian control women for associations with four candidate genes: follistatin, CYP19 (aromatase), CYP17a, and the insulin receptor (INSR). These genes were analyzed using microsatellite markers located near or inside the genes. We found that only the insulin receptor gene marker D19S884 was significantly associated with PCOS (p=0.006 and even after a conservative correction p=0.042). The INSR gene region was then fine mapped with an additional panel of 9 markers but only marker D19S884, located 1 cM telomeric to the INSR gene, was again associated with PCOS. In conclusion, our results suggested that a susceptibility gene for PCOS was located on chromosome 19p13.3 in the insulin receptor gene region. It remains to be determined if this susceptibility gene is the insulin receptor gene itself or a closely located gene. Since insulin stimulates androgen secretion by the ovarian stroma it is likely that INSR function in the ovary is involved in the genetic susceptibility ot PCOS.
Tongue Base Reduction with Thyro-Hyoido-Pexy (TBRTHP) vs. Tongue Base Reduction with Hyo-Epiglottoplasty (TBRHE) in mild-severe OSAHS adult treatment. Preliminary findings from a prospective randomised trial. (2010)

In a preliminary prospective randomised study, a series of 5 patients submitted to classic Tongue Base Reduction with Hyo-Epiglottoplasty (TBRHE according to Chabolle et al., 1998) is compared to a series of 7 patients submitted to a modified version of Chabolle's procedure. The changes introduced in the new surgical technique can be summarised as follows: a) lower neck skin incision; b) different neurovascular bundle identification; c) submucosal tongue base muscle resection; d) variation of the caudal hyoid stabilisation, already described by the Authors in 2008 (Tongue Base Reduction with Thyro-Hyoido-Pexy). The objective has been primarily to compare the feasibility, functional effectiveness and overall tolerability of the modified procedure. In this preliminary study Tongue Base Reduction with Thyro-Hyoido-Pexy has proven to be an easy and rapid procedure, with shorter post-operative functional recovery and comparable polysomnographic and neuro-psychological short time results.
Karyological Analysis and DNA Barcoding of Pompia Citron: A First Step toward the Identification of Its Relatives (2019)

Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the DNA content and to reconstruct the karyotype of several Pompia accessions. Molecular data from plastid DNA barcoding and nuclear DNA sequencing were used to study the genetic distance between Pompia and other citrus species. Flow cytometric estimates of DNA content and somatic chromosome counts suggest that Pompia is a regular diploid Citrus species. DNA polymorphisms of nuclear and chloroplast markers allowed us to investigate the genetic relationships between Pompia accessions and other Citrus species. Based on DNA polymorphism data we propose that Pompia is a very recent interspecific hybrid generated by a cross between <i>C. aurantium</i> (as seed bearer) and <i>C. medica</i> (as pollen donor). Our findings pave the way for further and more specific investigations of local Pompia germplasm resources that may help the preservation and valorisation of this valuable citrus fruit tree.
Removal of an intron with unique 3′ branch site creates an amino-terminal protein sequence directing the scERV1 gene product to mitochondria (1996)

The yeast scERV1 gene is of special interest because it has a dual function in mitochondrial biogenesis and in the regulation of the cell cycle. The recent discovery that the yeast scERV1 gene has a structural and functional human homologue initiated a detailed comparison of the genes and their structures. In addition the homologous ALR (augmenter of liver regeneration) genes from rat and mouse have just been identified and it has been found that the mammalian proteins have a specific function in liver regeneration and in spermatogenesis. It now turns out that the organization of the 5' regions of these genes is much more complicated than expected. The latest research has discovered an additional intron in the 5' region of the mouse gene and possible amino-terminal extensions of the reading frames. In this work, reinvestigation of the 5' region of the yeast gene identifies a putative intron with an unusual 3' branch site. It is shown that a small intron of 83 nucleotides is present in this genomic region. Analysis of cDNA clones demonstrates that the intron is correctly removed from the messenger RNA and that therefore the unusual 3' branch site is probably functional. Furthermore, studies with antibodies directed against recombinant scERV1 protein demonstrate that the gene product is associated with mitochondria, in agreement with its involvement in mitochondrial biogenesis. Complementation experiments with mutants and different 5' deletions of the gene identify the corresponding promotor for transcription and the start codon for translation.
Forecasting: theory and practice (2022)

Forecasting has always been at the forefront of decision making and planning. The uncertainty that surrounds the future is both exciting and challenging, with individuals and organisations seeking to minimise risks and maximise utilities. The large number of forecasting applications calls for a diverse set of forecasting methods to tackle real-life challenges. This article provides a non-systematic review of the theory and the practice of forecasting. We provide an overview of a wide range of theoretical, state-of-the-art models, methods, principles, and approaches to prepare, produce, organise, and evaluate forecasts. We then demonstrate how such theoretical concepts are applied in a variety of real-life contexts. We do not claim that this review is an exhaustive list of methods and applications. However, we wish that our encyclopedic presentation will offer a point of reference for the rich work that has been undertaken over the last decades, with some key insights for the future of forecasting theory and practice. Given its encyclopedic nature, the intended mode of reading is non-linear. We offer cross-references to allow the readers to navigate through the various topics. We complement the theoretical concepts and applications covered by large lists of free or open-source software implementations and publicly-available databases. © 2021 The Author(s)
Extraction of Rare Earth Elements with sec-Octylphenoxy Acetic Acid in n-Heptane (2000)

The extraction mechanism of rare earth elements from chloride medium with sec octylphenoxy acetic acid(CA 12) in n heptane has been studied. The results showed that CA 12 could be applied to separation of Y from light rare earth mixture. The structures of the extracted complexes were deduced based on the IR measurements.
A programmable dynamic interconnection network router with hidden refresh (1998)

A VLSI implementation of a programmable pipelined router scheme for parallel machine interconnection networks is presented in this paper. The implementation is based on a dynamic content-addressable memory (DCAM) that supports unique bit masking per entry. The number of required DCAM entries is extremely small; it is of the same order as the node degree (output ports). This, in turn, makes it possible to implement a dynamic content-addressable memory in order to reduce the physical size of the system. A DCAM is implemented with only six and a half transistors (one transistor is shared by two cells). We have provided circuitry and arranged timing to achieve refreshing of the stored data in a hidden fashion. In addition to the DCAM, we have incorporated a fast priority scheme that allows only one entry to he selected. The router executes routing algorithms in 1.5 clock cycles, this being the fastest approach for flexible routers. The prototype router has 24 entries, and is able to sustain a throughput of one routing decision per cycle.
Inflammatory Gene Expression Patterns Revealed by DNA Microarray Analysis in TNF-α-treated SGBS Human Adipocytes (2006)

We report here the use of human inflammation arrays to study the inflammatory gene expression profile of TNF-alpha- treated human SGBS adipocytes. Human preadipocytes (SGBS) were induced to differentiate in primary culture, and adipocyte differentiation was confirmed, using Oil Red O staining. We treated the differentiated adipocytes with TNF-alpha, and RNA from differentiated adipocytes with or without TNF-alpha treatment was hybridized to MWG human inflammation arrays to compare expression profiles. Eleven genes were up- or down-regulated in TNF-alpha-treated adipocytes. As revealed by array analysis, among 6 up-regulated genes, only eotaxin-1, monocyte chemoattractant protein-1 (MCP-1), and vascular cell adhesion molecule 1 isoform a precursor (VCAM1) were confirmed by real-time polymerase chain reaction (PCR). Similarly, among 5 down-regulated genes, only IL-1 family member 5 (IL1F5), a disintegrin and metalloprotease with thrombospondin motifs-1 preproprotein (ADAMTS1), fibronectin 1 isoform 1 preprotein (FN1), and matrix metalloproteinase 15 preprotein (MMP15) were confirmed by real-time PCR. There was a substantial increase (50-fold) in eotaxin-1 in response to TNF-alpha. Taken together, we have identified several inflammatory molecules expressed in SGBS adipocytes and discovered molecular factors explaining the relationship between obesity and atherosclerosis, focusing on inflammatory cytokines expressed in the TNF-alpha-treated SGBS cells. Further investigation into the role of these up- or down-regulated cytokine genes during the pathological processes leading to the development of atherosclerosis is warranted.