gebhart/patrepeval huggingface dataset:
The Diagnostic Applications of Saliva— A Review (2002)

This review examines the diagnostic application of saliva for systemic diseases. As a diagnostic fluid, saliva offers distinctive advantages over serum because it can be collected non-invasively by individuals with modest training. Furthermore, saliva may provide a cost-effective approach for the screening of large populations. Gland-specific saliva can be used for diagnosis of pathology specific to one of the major salivary glands. Whole saliva, however, is most frequently used for diagnosis of systemic diseases, since it is readily collected and contains serum constituents. These constituents are derived from the local vasculature of the salivary glands and also reach the oral cavity via the flow of gingival fluid. Analysis of saliva may be useful for the diagnosis of hereditary disorders, autoimmune diseases, malignant and infectious diseases, and endocrine disorders, as well as in the assessment of therapeutic levels of drugs and the monitoring of illicit drug use.
The Role of Etching in the Formation of Ag Nanoplates with Straight, Curved and Wavy Edges and Comparison of Their SERS Properties (2013)

We investigate the role of etching in the formation of Ag nanoplates with different morphologies. By examining the reduction of AgNO3 with poly(vinyl pyrrolidone) in an aqueous solution under a hydrothermal condition, we confirm that etching plays an essential role in promoting the growth of Ag triangular nanoplates with straight edges at the expense of multiple twinned particles via Ostwald ripening. Once all the multiple twinned particles are gone, etching will continue at the corners of nanoplates, leading to the formation of enneahedral nanoplates with curved edges. When the nanoplates with straight edges are transferred into ethanol and subjected to a solvothermal treatment, we obtain nanoplates with wavy edges and sharp corners due to etching on the edges. A comparison study indicates that, at the same particle concentration, Ag nanoplates with wavy edges embraces a SERS enhancement factor at least 6 and 13 times stronger than those with straight and curved edges, respectively. The results from finite difference time domain calculations support our experimental observation that the sharp features on nanoplates with wavy edges are the most active sites for SERS.
High-power double-clad fiber lasers (1993)

Rare-earth doped, laser-diode-pumped, single-mode, double-clad fiber lasers are studied in detail, experimentally and theoretically, with particular attention to properties of scaling to higher output powers. Gain saturation, spontaneous emission, fiber propagation loss, and the optimum output coupler are considered for oscillator design and laser performance. Thermal properties are investigated, including the thermal fracture limit, the decrease of quantum efficiency with increasing pump power through the temperature dependence of multiphonon decay and ion-ion energy transfer, and thermal lensing. Self-focusing and Raman effects are briefly considered. It is shown that output powers in the tens of watts range are readily feasible with available double-clad fiber lasers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nuclear Hormone Receptor NHR-49 controls a HIF-1-independent hypoxia adaptation pathway in Caenorhabditis elegans (2021)

Abstract The response to insufficient oxygen (hypoxia) is orchestrated by the conserved Hypoxia-Inducible Factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel to HIF to mediate the physiological hypoxia response. Here, we describe a HIF-independent hypoxia response pathway controlled by Caenorhabditis elegans Nuclear Hormone Receptor NHR-49, an orthologue of mammalian Peroxisome Proliferator-Activated Receptor alpha (PPARα). We show that nhr-49 is required for worm survival in hypoxia and is synthetic lethal with hif-1 in this context, demonstrating that these factors act independently. RNA-seq analysis shows that in hypoxia nhr-49 regulates a set of genes that are hif-1- independent, including autophagy genes that promote hypoxia survival. We further show that Nuclear Hormone Receptor nhr-67 is a negative regulator and Homeodomain-interacting Protein Kinase hpk-1 is a positive regulator of the NHR-49 pathway. Together, our experiments define a new, essential hypoxia response pathway that acts in parallel to the well-known HIF-mediated hypoxia response.
Direct Importance Estimation with Model Selection and Its Application to Covariate Shift Adaptation (2007)

A situation where training and test samples follow different input distributions is called covariate shift. Under covariate shift, standard learning methods such as maximum likelihood estimation are no longer consistent-weighted variants according to the ratio of test and training input densities are consistent. Therefore, accurately estimating the density ratio, called the importance, is one of the key issues in covariate shift adaptation. A naive approach to this task is to first estimate training and test input densities separately and then estimate the importance by taking the ratio of the estimated densities. However, this naive approach tends to perform poorly since density estimation is a hard task particularly in high dimensional cases. In this paper, we propose a direct importance estimation method that does not involve density estimation. Our method is equipped with a natural cross validation procedure and hence tuning parameters such as the kernel width can b e objectively optimized. Simulations illustrate the usefulness of our approach.
Nonpatentable drugs and the cost of our ignorance (2006)

The pharmaceutical industry spends over US$10 billion to fund some 90% of the 40 000–80 000 randomized controlled clinical trials (RCTs) being conducted across the world at any given time.[1][1],[2][2],[3][3] By its own estimation, the pharmaceutical industry in Canada spent Can$501.8 million on
Immune-checkpoint proteins VISTA and PD-1 nonredundantly regulate murine T-cell responses (2015)

V-domain immunoglobulin suppressor of T-cell activation (VISTA) is a negative immune-checkpoint protein that suppresses T-cell responses. To determine whether VISTA synergizes with another immune-checkpoint, programmed death 1 (PD-1), this study characterizes the immune responses in VISTA-deficient, PD-1-deficient (KO) mice and VISTA/PD-1 double KO mice. Chronic inflammation and spontaneous activation of T cells were observed in both single KO mice, demonstrating their nonredundancy. However, the VISTA/PD-1 double KO mice exhibited significantly higher levels of these phenotypes than the single KO mice. When bred onto the 2D2 T-cell receptor transgenic mice, which are predisposed to development of inflammatory autoimmune disease in the CNS, the level of disease penetrance was significantly enhanced in the double KO mice compared with in the single KO mice. Consistently, the magnitude of T-cell response toward foreign antigens was synergistically higher in the VISTA/PD-1 double KO mice. A combinatorial blockade using monoclonal antibodies specific for VISTA and PD-L1 achieved optimal tumor-clearing therapeutic efficacy. In conclusion, our study demonstrates the nonredundant role of VISTA that is distinct from the PD-1/PD-L1 pathway in controlling T-cell activation. These findings provide the rationale to concurrently target VISTA and PD-1 pathways for treating T-cell-regulated diseases such as cancer.
Detachable fiber optic tips for use in thulium fiber laser lithotripsy (2013)

The thulium fiber laser (TFL) has recently been proposed as an alternative to the Holmium:YAG (Ho:YAG) laser for lithotripsy. The TFL's Gaussian spatial beam profile provides higher power transmission through smaller optical fibers with reduced proximal fiber tip damage, and improved saline irrigation and flexibility through the ureteroscope. However, distal fiber tip damage may still occur during stone fragmentation, resulting in disposal of the entire fiber after the procedure. A novel design for a short, detachable, distal fiber tip that can fit into an ureteroscope's working channel is proposed. A prototype, twist-lock, spring-loaded mechanism was constructed using micromachining methods, mating a 150-μm-core trunk fiber to 300-μm-core fiber tip. Optical transmission measuring 80% was observed using a 30-mJ pulse energy and 500-μs pulse duration. Ex vivo human calcium oxalate monohydrate urinary stones were vaporized at an average rate of 187 μg/s using 20-Hz modulated, 50% duty cycle 5 pulse packets. The highest stone ablation rates corresponded to the highest fiber tip degradation, thus providing motivation for use of detachable and disposable distal fiber tips during lithotripsy. The 1-mm outer-diameter prototype also functioned comparable to previously tested tapered fiber tips.
Identification of a Novel Pool of Extracellular Pro-myostatin in Skeletal Muscle (2008)

Myostatin, a transforming growth factor-beta superfamily ligand, negatively regulates skeletal muscle growth. Generation of the mature signaling peptide requires cleavage of pro-myostatin by a proprotein convertase, which is thought to occur constitutively in the Golgi apparatus. In serum, mature myostatin is found in an inactive, non-covalent complex with its prodomain. We find that in skeletal muscle, unlike serum, myostatin is present extracellularly as uncleaved pro-myostatin. In cultured cells, co-expression of pro-myostatin and latent transforming growth factor-beta-binding protein-3 (LTBP-3) sequesters pro-myostatin in the extracellular matrix, and secreted pro-myostatin can be cleaved extracellularly by the proprotein convertase furin. Co-expression of LTBP-3 with myostatin reduces phosphorylation of Smad2, and ectopic expression of LTBP-3 in mature mouse skeletal muscle increases fiber area, consistent with reduction of myostatin activity. We propose that extracellular pro-myostatin constitutes the major pool of latent myostatin in muscle. Post-secretion activation of this pool by furin family proprotein convertases may therefore represent a major control point for activation of myostatin in skeletal muscle.
Signal Transduction by the TGF-β Superfamily (2002)

Transforming growth factor-beta (TGF-beta) superfamily members regulate a plethora of developmental processes, and disruption of their activity has been implicated in a variety of human diseases ranging from cancer to chondrodysplasias and pulmonary hypertension. Intense investigations have revealed that SMAD proteins constitute the basic components of the core intracellular signaling cascade and that SMADs function by carrying signals from the cell surface directly to the nucleus. Recent insights have revealed how SMAD proteins themselves are regulated and how appropriate subcellular localization of SMADs and TGF-beta transmembrane receptors is controlled. Current research efforts investigating the contribution of SMAD-independent pathways promise to reveal advances to enhance our understanding of the signaling cascade.
HIV-1 Cell to Cell Transfer across an Env-induced, Actin-dependent Synapse (2004)

Direct cell-cell transfer is an efficient mechanism of viral dissemination within an infected host, and human immunodeficiency virus 1 (HIV-1) can exploit this mode of spread. Receptor recognition by HIV-1 occurs via interactions between the viral surface envelope glycoprotein (Env), gp120, and CD4 and a chemokine receptor, CCR5 or CXCR4. Here, we demonstrate that the binding of CXCR4-using HIV-1-infected effector T cells to primary CD4(+)/CXCR4(+) target T cells results in rapid recruitment to the interface of CD4, CXCR4, talin, and lymphocyte function-associated antigen 1 on the target cell, and of Env and Gag on the effector cell. Recruitment of these membrane molecules into polarized clusters was dependent on Env engagement of CD4 and CXCR4 and required remodelling of the actin cytoskeleton. Transfer of Gag from effector to target cell was observed by 1 h after conjugate formation, was independent of cell-cell fusion, and was probably mediated by directed virion fusion with the target cell. We propose that receptor engagement by Env directs the rapid, actin-dependent recruitment of HIV receptors and adhesion molecules to the interface, resulting in a stable adhesive junction across which HIV infects the target cell.
Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development (1999)

It is critical to expand the preclinical development of new drugs to include the assessment of their activity against currently circulating highly drug-resistant clinical strains, in order to develop appropriate salvage therapies for patients harboring resistant strains.
The Btk Inhibitor, PCI-32765, Induces Durable Responses with Minimal Toxicity In Patients with Relapsed/Refractory B-Cell Malignancies: Results From a Phase I Study (2010)

Abstract Abstract 964 Introduction: Bruton's tyrosine kinase (Btk) is a downstream mediator of B-cell receptor signaling. PCI-32765 is a potent, selective, irreversible and orally bioavailable small molecule inhibitor of Btk. We have previously reported initial efficacy and safety data with this agent in various B-cell malignancies (ASCO 2010 abstract # 8012). We now report updated efficacy and safety of PCI-32765 in patients (pts) with long-term dosing. Pts and Methods: Pts on the Phase 1 study were treated with escalating doses over 6 cohorts. Cohort 1 was dosed at 1.25 mg/kg/day with subsequent dose escalation (2.5, 5.0, 8.3, 8.3 continuous dosing, and 12.5 mg/kg/day) based on safety evaluation. Pts were analyzed according to histology, pretreatment clinical and laboratory characteristics, PCI-32765 dose levels, overall response (OR), and response duration. Results: Responses and time on study (≥ 6 months) are summarized in Table 1. Of 47 pts enrolled in the Phase 1 study, 20 pts (43%) achieved an OR including 3 complete remissions (CR) and 17 partial remissions (PR). Fourteen of 47 pts have been on study ≥ 6 months; of these 8 pts demonstrated a PR or better and 6 pts maintained stable disease (SD). Responses were observed irrespective of pretreatment risk factors such as performance status, lactate dehydrogenase (LDH) levels, or disease burden. Durable responses were seen at all dose levels and across various histologic subtypes (Table 1) and currently 9 of 14 pts with treatment ≥ 6 months are still on study. Study-drug related Grade ≥ 3 toxicities were reported in 9/47 pts (19%). Five of 47 pts discontinued study drug due to adverse events: neutropenia (Grade 3) lasting &gt; 7 days, hypersensitivity reaction (Grade 3), small bowel obstruction (Grade 3), anemia (Grade 2), and exacerbation of chronic obstructive pulmonary disease (Grade 3). No evidence of cumulative hematologic toxicity or long-term safety signals have been observed. No treatment-related deaths have been reported. Conclusion: PCI-32765 is a novel oral Btk inhibitor that induces durable objective responses in various relapsed or refractory B-cell malignancies. The favorable safety profile and lack of cumulative hematologic toxicities support further studies of both monotherapy and combination treatment with PCI-32765. Disclosures: Fowler: Pharmacyclics: Consultancy, Research Funding. Off Label Use: This phase I trial describes the results of a first in human Phase I trial. This drug is not FDA approved for the treatment of malignancy. Sharman:Pharmacyclics, Inc: Honoraria, PI grant. Smith:pharmacyclics: Research Funding. Boyd:pharmacyclics: Research Funding. Grant:pharmacyclics: Research Funding. Kolibaba:pharmacyclics: Research Funding. Furman:Pharmacyclics, Inc: Research Funding. Buggy:pharmacyclics: Employment. Loury:Pharmacyclics: Employment, Equity Ownership. Hamdy:pharmacyclics: Employment. Advani:Pharmacyclics, Inc: Honoraria, PI grant.
Utilizacao de farinha obtida a partir de rejeito de batata na elaboracao de biscoitos (2005)

A industria de batata cozida a vapor, embalada a vacuo e esterilizada, gera uma quantidade apreciavel de residuos. O objetivo deste trabalho foi estudar a viabilidade da utilizacao deste residuo, fornecido pela industria, na obtencao de farinha para a elaboracao de biscoitos, agregando valor ao que atualmente e destinado para alimentacao animal. Para cada 100 gramas do residuo fresco foram obtidos 18 gramas de farinha com 6,8% de umidade. Substituiu-se, na formulacao original do biscoito, 25% da fecula de mandioca pela farinha de batata. A media geral para a analise de aceitabilidade do biscoito de batata, feita com cento e dois provadores nao treinados, foi 8,0 (oito) indicando boa aceitacao do produto e a possibilidade de utilizacao do residuo. Palavras-chave: aproveitamento de residuos; batata; biscoito; analise sensorial
Semaphorin-4D (Sema-4D), the Plexin-B1 ligand, is involved in mouse ovary follicular development (2007)

In the ovarian follicle, the effect of Plexin-B1 is mediated by sema-4D.
Comparison of hyperspectral sub-pixel detection with and without a priori knowledge of target features (2002)

Hyperspectral sensors collect imagery simultaneously in hundreds of contiguous bands. They provide a unique mixture of spectral and spatial information to detect and identify materials and targets, even targets that are much smaller than a pixel. The ability to perform sub-pixel detection allows hyperspectral systems to perform wide-area search to direct other assets to areas of interest. For example HSI sensors can be used to cue narrow-field, high-spatial resolution E-O cameras or focus the attention of image analysts on target regions. Several algorithms have been developed at TRW to perform target detection based on the spectral information in a scene, each assuming a different level of a priori knowledge about materials present in the scene. This paper describes results obtained applying these algorithms to an HSI data set collected with the HYDICE sensor.
24-nor-Ursane Type Triterpenoids from the Stems of Rumex japonicus (2005)

Fractionation of an EtOAc-soluble extract of the stems of Rumex japonicus led to the isolation of two new 24-norursane type triterpenoids, 2alpha,3alpha,19alpha-trihydroxy-24-norurs-4(23),12-dien-28-oic acid (1) and 4(R),23-epoxy-2alpha,3alpha,19alpha-trihydroxy-24-norurs-12-en-28-oic acid (2), along with the known compounds myrianthic acid (3), tormentic acid, and emodin. The structures of 1 and 2 were elucidated by spectroscopic methods, particularly by extensive 1D and 2D NMR studies.
Identification and Functional Expression of a Receptor Selectively Recognizing Parathyroid Hormone, the PTH2 Receptor (1995)

We have identified a G-protein-coupled receptor specifically activated by parathyroid hormone, which we refer to as the PTH2 receptor. Parathyroid hormone (PTH) and parathyroid hormone-related peptide (PTHrP, hypercalcemia of malignancy factor) activate a previously identified PTH/PTHrP receptor, which has a widespread tissue distribution. The PTH2 receptor is much more selective in ligand recognition and appears to have a more specific tissue distribution. It is activated by PTH and not by PTHrP and is particularly abundant in the brain and pancreas.
Targeted inhibition of tumor-specific glutaminase diminishes cell-autonomous tumorigenesis (2015)

Glutaminase (GLS), which converts glutamine to glutamate, plays a key role in cancer cell metabolism, growth, and proliferation. GLS is being explored as a cancer therapeutic target, but whether GLS inhibitors affect cancer cell-autonomous growth or the host microenvironment or have off-target effects is unknown. Here, we report that loss of one copy of Gls blunted tumor progression in an immune-competent MYC-mediated mouse model of hepatocellular carcinoma. Compared with results in untreated animals with MYC-induced hepatocellular carcinoma, administration of the GLS-specific inhibitor bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES) prolonged survival without any apparent toxicities. BPTES also inhibited growth of a MYC-dependent human B cell lymphoma cell line (P493) by blocking DNA replication, leading to cell death and fragmentation. In mice harboring P493 tumor xenografts, BPTES treatment inhibited tumor cell growth; however, P493 xenografts expressing a BPTES-resistant GLS mutant (GLS-K325A) or overexpressing GLS were not affected by BPTES treatment. Moreover, a customized Vivo-Morpholino that targets human GLS mRNA markedly inhibited P493 xenograft growth without affecting mouse Gls expression. Conversely, a Vivo-Morpholino directed at mouse Gls had no antitumor activity in vivo. Collectively, our studies demonstrate that GLS is required for tumorigenesis and support small molecule and genetic inhibition of GLS as potential approaches for targeting the tumor cell-autonomous dependence on GLS for cancer therapy.
Urinary Biomarkers for Sensitive and Specific Detection of Acute Kidney Injury in Humans (2008)

Acute kidney injury (AKI) is associated with high morbidity and mortality. The lack of sensitive and specific injury biomarkers has greatly impeded the development of therapeutic strategies to improve outcomes of AKI.The unique objective of this study was to evaluate the diagnostic performance of nine urinary biomarkers of AKI-kidney injury molecule-1 (KIM-1), neutrophil gelatinase associated lipocalin (NGAL), interleukin-18 (IL-18), hepatocyte growth factor (HGF), cystatin C (Cys), N-acetyl-beta-D-glucosaminidase (NAG), vascular endothelial growth factor (VEGF), chemokine interferon-inducible protein 10 (IP-10; CXCL10), and total protein-in a cross-sectional comparison of 204 patients with or without AKI.Median urinary concentrations of each biomarker were significantly higher in patients with AKI than in those without AKI (p < 0.001). The area under the receiver operating characteristics curve (AUC-ROC) for the combination of biomarkers using a logic regression model [risk score of 2.93*(NGAL > 5.72 and HGF > 0.17) + 2.93*(PROTEIN > 0.22) -2*(KIM < 0.58)] was greater (0.94) than individual biomarker AUC-ROCs. Age-adjusted levels of urinary KIM-1, NAG, HGF, VEGF, and total protein were significantly higher in patients who died or required renal replacement therapy (RRT) when compared to those who survived and did not require RRT.Our results demonstrate the comparative value of multiple biomarkers in the diagnosis and prognosis of AKI.
Role of Hcp, a type 6 secretion system effector, of Aeromonas hydrophila in modulating activation of host immune cells (2010)

Recently, we reported that the type 6 secretion system (T6SS) of Aeromonas hydrophila SSU plays an important role in bacterial virulence in a mouse model, and immunization of animals with the T6SS effector haemolysin co-regulated protein (Hcp) protected them against lethal infections with wild-type bacteria. Additionally, we showed that the mutant bacteria deleted for the vasH gene within the T6SS gene cluster did not express the hcp gene, while the vasK mutant could express and translocate Hcp, but was unable to secrete it into the extracellular milieu. Both of these A. hydrophila SSU mutants were readily phagocytosed by murine macrophages, pointing to the possible role of the secreted form of Hcp in the evasion of the host innate immunity. By using the ΔvasH mutant of A. hydrophila, our in vitro data showed that the addition of exogenous recombinant Hcp (rHcp) reduced bacterial uptake by macrophages. These results were substantiated by increased bacterial virulence when rHcp was added along with the ΔvasH mutant in a septicaemic mouse model of infection. Analysis of the cytokine profiling in the intraperitoneal lavage as well as activation of host cells after 4&emsp14;h of infection with the ΔvasH mutant supplemented with rHcp indicated that this T6SS effector inhibited production of pro-inflammatory cytokines and induced immunosuppressive cytokines, such as interleukin-10 and transforming growth factor-β, which could circumvent macrophage activation and maturation. This mechanism of innate immune evasion by Hcp possibly inhibited the recruitment of cellular immune components, which allowed bacterial multiplication and dissemination in animals, thereby leading to their mortality.