Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial Rescue of the KIT-Deficient Testicular Phenotype in KitW‑v/KitW‑v Tg(TSPY) Mice1

TSPY encodes the testis-specific protein Y-linked. In man, expression of TSPY is restricted to the testis, where TSPY is expressed in spermatogonia, primary spermatocytes, and round spermatids, and to the prostate gland. There is circumstantial evidence that TSPY is involved in spermatogonial proliferation and gonadal tumorigenesis. Because the laboratory mouse carries the Tspy gene in a naturally silenced state (Tspy-ps), we previously restored TSPY activity in mice and generated a TSPY transgenic mouse line in which the organization and expression of the human TSPY transgene follow the human pattern. In the present study, we generated TSPY transgenic KIT-deficient KitW‑v/KitW‑v mice and analyzed the histology of the testes and epididymides in order to contribute to understanding TSPY function in early germ cell development and spermatogenesis. The KIT receptor and its ligand KITL, previously called stem cell factor, have an indispensable role in hematopoiesis, melanogenesis, and gametogenesis. Homozygous KitW-v mutant male mice on a C57BL/6J background with a mutation in the Kit gene are infertile due to an almost total loss of germ cells in the testes. In this study, histological analyses of testes and epididymides showed an increased number of meiotic and postmeiotic germ cells in KitW‑v/KitW‑v Tg(TSPY) mice compared with age-matched KitW‑v/KitW‑v controls. TSPY was able to restore fertility of some but not all TSPY transgenic KitW‑v/KitW‑v males. Our findings show that TSPY is able to partially rescue spermatogenesis and fertility of KitW‑v/KitW‑v mutants and thereby point to a putative role of TSPY in fetal and adult germ cell proliferation.
Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat

We isolated clones and determined the sequence of portions of mouse and human cellular DNA which cross-hybridize strongly with the IR3 repetitive region of Epstein-Barr virus. The sequences were found to be tandem arrays of a simple sequence based on the triplet GGA, very similar to the IR3 repeat. The cellular repeats have distinct differences from the viral repeat region, however, and their sequences do not appear capable of being translated into a purely glycine-plus-alanine protein domain like the portion of the Epstein-Barr nuclear antigen coded by IR3. Although the relationship between IR3 and the cellular repeats is left unclear, the cellular repeats have many interesting features. The tandem arrays are about 1 to several kilobases long, much shorter than satellite tandem repeats and larger than other interspersed, tandem repeats. Each of the repeats is a distinct variation, perhaps diverged from a common sequence, (GGA)n. This family is present in the genomes of all species tested and appears to be a ubiquitous feature of all higher eucaryotic genomes.
In vivo evaluation of ocular demodicosis using laser scanning confocal microscopy.

PURPOSE To investigate the applicability of in vivo laser scanning confocal microscopy in the diagnosis and follow-up of ocular demodicosis infestation in a prospective controlled study. METHODS Fifteen right eyes of 15 patients with blepharitis associated with cylindrical dandruff (10 males, 5 females; mean age: 62.9 ± 9 years) and eight right eyes of eight age- and sex-matched control subjects underwent HRTII/RCM, evaluation of ocular symptom scores, tear function tests including vital stainings, Schirmer test, and tear clearance test, and evaluation of mite numbers in the eyelids. RESULTS In vivo confocal microscopy effectively disclosed the mites in the terminal bulbs of the eyelashes, which were not observed after treatment. Eyelids with demodicosis infestation showed marked inflammatory infiltrates around the meibomian glands and conjunctiva, which cleared with tea tree oil treatment. CONCLUSIONS Laser scanning confocal microscopy seems to be an efficient noninvasive tool in the diagnosis and follow-up of ocular demodicosis infestation.
CCR5, GPR15, and CXCR6 Are Major Coreceptors of Human Immunodeficiency Virus Type 2 Variants Isolated from Individuals with and without Plasma Viremia

ABSTRACT Human immunodeficiency virus type 2 (HIV-2) is generally considered capable of using a broad range of coreceptors. Since HIV-2 variants from individuals with nonprogressive infection were not studied previously, the possibility that broad coreceptor usage is a property of variants associated with progressive infection could not be excluded. To test this, we determined the coreceptor usage of 43 HIV-2 variants isolated from six long-term-infected individuals with undetectable plasma viremia. Using GHOST indicator cells, we showed for the first time that the only coreceptors efficiently used by low-pathogenic HIV-2 variants are CCR5, GPR15 (BOB), and CXCR6 (BONZO). Surprisingly, control HIV-2 variants (n = 45) isolated from seven viremic individuals also mainly used these three coreceptors, whereas use of CCR1, CCR2b, or CCR3 was rare. Nearly a quarter of all HIV-2 variants tested could infect the parental GHOST cells, which could be partially explained by CXCR4 usage. Use of CXCR4 was observed only for HIV-2 variants from viremic individuals. Thirty-eight variants from aviremic and viremic HIV-2-infected individuals were additionally tested in U87 cells. All except one were capable of infecting the parental U87 cells, often with high efficiency. When virus production in parental cells was regarded as background in the coreceptor-transduced cell lines, the results in U87 cells were largely in agreement with the findings in GHOST cells. HIV-2 isolates from aviremic individuals commonly use as coreceptors CCR5, GPR15, and CXCR6, as well as an unidentified receptor expressed by U87 cells. Broad coreceptor usage, therefore, does not appear to be associated with pathogenicity of HIV-2.
Chlorination of Pyridinium Compounds

Reactive oxygen species produced by activated neutrophils and monocytes are thought to be involved in mediating the loss of collagen and other matrix proteins at sites of inflammation. To evaluate their potential to oxidize the pyridinoline (Pyd) cross-links found in collagen types I and II, we reacted hydrogen peroxide (H2O2), hypochlorous acid/hypochlorite (HOCl/OCl−), and singlet oxygen (O2(1Δg)) with the Pyd substitutes, pyridoxamine dihydrochloride and vitamin B6, which share the same chemical structure and spectral properties of Pyd cross-links. Neither H2O2 (125–500 μm) nor O2(1Δg) (10–25 μm) significantly changed the spectral properties of pyridoxamine or vitamin B6. Reaction of HOCl/OCl− (12.5–50 μm) with pyridoxamine at pH 7.2 resulted in a concentration-dependent appearance of two new absorbance peaks and a decrease in fluorescence at 400 nm (excitation 325 nm). The new absorbance peaks correlated with the formation of anN-chloramine and the product of its subsequent reaction with pyridoxamine. In contrast, the extent to which HOCl reacted with vitamin B6, which lacks a primary amine group, was variable at this pH. At lysosomal pH 5.5, Cl2/HOCl/OCl− reacted with both pyridoxamine and vitamin B6. Four of the chlorinated products of this reaction were identified by gas chromatography-mass spectrometry and included 3-chloropyridinium, an aldehyde, and several chlorinated products with disrupted rings. To evaluate the effects of Cl2/HOCl/OCl− on Pyd cross-links in collagen, we exposed bone collagen type I and articular cartilage type II to HOCl. Treatment of either collagen type with HOCl at pH 5.0 or 7.2 resulted in the oxidation of amine groups and, for collagen type II, the specific decrease in Pyd cross-link fluorescence, suggesting that during inflammation both oxidations may be used by neutrophils and monocytes to promote the loss of matrix integrity.
Evidence for a defect of antibody-dependent cellular cytotoxic (ADCC) effector function and anti-HIV gp120/41-specific ADCC-mediating antibody titres in HIV-infected individuals.

Antibody-dependent cellular cytotoxicity (ADCC) is an important antiviral effector mechanism. However, its role, as well as the functional integrity of the ADCC-effector cells in HIV infections, is not well understood. For studying gp120/41-specific ADCC, we recently developed a virus-free target cell system, using a natural killer (NK) cell activity-resistant human lymphoid cell line of B lineage, which was transfected with the env gene of the human immunodeficiency virus type 1 (HIV-1); gp120/41-expressing cell clones were thus selected. In this study, these gp120/41-expressing cloned cells were used as targets in a gp120/41-specific ADCC assay for (a) examining the functional integrity of ADCC-effector cells from HIV-seropositive individuals, and (b) titrating the sera of these individuals for gp120/41-specific, ADCC-mediating antibodies. Our data indicate for the first time that the percentage of sera positive for ADCC-mediating antibodies to gp120/41 is higher in individuals with CD4 counts < or = 400 and > or = 200/mm3. The individuals with CD4 counts < 200/mm3 were found to have the lowest titers of these antibodies in their sera. The ADCC-effector function of the peripheral blood mononuclear cells (PBMC) of HIV-infected individuals was significantly (p < 0.05) reduced as compared to the PBMC from healthy, HIV-seronegative individuals. Further, human recombinant IL2 and interferon-gamma were found to exert a significant (p < 0.05) enhancing effect on ADCC mediated by PBMC from these HIV-infected individuals. (ABSTRACT TRUNCATED AT 250 WORDS)
Multilocus Sequence Typing of Serially Collected Isolates of Cryptococcus from HIV-Infected Patients in South Africa

ABSTRACT Patients with cryptococcal meningitis in sub-Saharan Africa frequently relapse following treatment. The natural history and etiology of these recurrent episodes warrant investigation. Here, we used multilocus sequence typing (MLST) to compare the molecular genotypes of strains of Cryptococcus neoformans and Cryptococcus gattii isolated from serial episodes of cryptococcal meningitis that were separated by at least 110 days. The most common MLST genotypes among the isolates were the dominant global clinical genotypes (M5 and M4) of molecular type VNI, as well as the VNI genotypes apparently restricted to southern Africa. In addition, there was considerable genetic diversity among these South African isolates, as 15% of the patients had unique genotypes. Eleven percent of the patients were reinfected with a genetically different strain following their initial diagnosis and treatment. However, the majority of serial episodes (89%) were caused by strains with the same genotype as the original strain. These results indicate that serial episodes of cryptococcosis in South Africa are frequently associated with persistence or relapse of the original infection. Using a reference broth microdilution method, we found that the serial isolates of 11% of the patients infected with strains of C. neoformans var. grubii with identical genotypes exhibited ≥4-fold increases in the MICs to fluconazole. Therefore, these recurrent episodes may have been precipitated by inadequate induction or consolidation of antifungal treatment and occasionally may have been due to increased resistance to fluconazole, which may have developed during the chronic infection.
Nutrition and Somatomedin: XVII. Circulating Somatomedin C During Treatment of Diabetic Ketoacidosis

Although somatomedin levels may be low in animals with experimental diabetes, values in humans have generally been normal. Because humans with severely decompensated diabetes have not been studied, we characterized somatomedin C responses during metabolic restoration in 21 patients with diabetic ketoacidosis. Somatomedin C values were compared with those of 25 outpatient controls. Somatomedin C in controls (mean ± SE) was 0.72 ± 0.09 U/ml, 69% of the mean sex-adjusted normal level; 28% of patients had values below the lower limit of normal. In ketoacidotic subjects, initial somatomedin C was 0.43 ± . 06 U/ml, 33% of the mean normal level; 52% of subjects had somatomedin C below the lower limit of normal. Initial levels in ketoacidotic subjects were unrelated to presenting levels of glucose, bicarbonate, ketones, or blood urea nitrogen but were significantly lower in patients of less than ideal body weight (0.30 vs. 0.58 U/ml, P < .03). Presenting levels of somatomedin C in ketoacidotic subjects were significantly lower than in controls (P <.02). During insulin-infusion therapy, somatomedin C rose to a peak of 1.16 ± 0.21 U/ml after 28 h, significantlyhigher than initial levels (P <.05). With continued subcutaneous insulin, somatomedin C fell to a nadir after an additional 22 h then rose more slowly to a final value of 0.75 ± 0.12 U/ml, significantly higher than the nadir (P <.05) but lower than peak values; final values in the ketoacidotic subjects were comparable to outpatient somatomedin C levels. Although final somatomedin C exhibited no apparent relationship to percent ideal body weight or final metabolic indices, values were lower in patients who had higher initial glucose (r = .43, P <.05). During the rapid rise of somatomedin C from initial to peak levels, somatomedin C values were correlated with levels of both bicarbonate (r = .37, P <.001) and ketones (r = −.31 , P <.005). Altered somatomedin C could not be attributed to changes in serum somatomedinbinding activity. Although improvement in somatomedin C levels over several days may be due to gradual intracellular normalization in response to subcutaneous insulin, the acute rise during the 1st day of intravenous therapy probably reflects rapid anabolic flux conferred by high levels of insulin and metabolic fuels. These findings establish a strong relationship between levels of somatomedin C and metabolic status in diabetic humans.
Transplantation of autologous synovial mesenchymal stem cells promotes meniscus regeneration in aged primates

Transplantation of aggregates of synovial mesenchymal stem cells (MSCs) enhanced meniscus regeneration in rats. Anatomy and biological properties of the meniscus depend on animal species. To apply this technique clinically, it is valuable to investigate the use of animals genetically close to humans. We investigated whether transplantation of aggregates of autologous synovial MSCs promoted meniscal regeneration in aged primates. Chynomolgus primates between 12 and 13 years old were used. After the anterior halves of the medial menisci in both knees were removed, an average of 14 aggregates consisting of 250,000 synovial MSCs were transplanted onto the meniscus defect. No aggregates were transplanted to the opposite knee for the control. Meniscus and articular cartilage were analyzed macroscopically, histologically, and by MRI T1rho mapping at 8 (n = 3) and 16 weeks (n = 4). The medial meniscus was larger and the modified Pauli's histological score for the regenerated meniscus was better in the MSC group than in the control group in each primate at 8 and 16 weeks. Mankin's score for the medial femoral condyle cartilage was better in the MSC group than in the control group in all primates at 16 weeks. T1rho value for both the regenerated meniscus and adjacent articular cartilage in the MSC group was closer to the normal meniscus than in the control group in all primates at 16 weeks. Transplantation of aggregates of autologous synovial MSCs promoted meniscus regeneration and delayed progression of degeneration of articular cartilage in aged primates. This is the first report dealing with meniscus regeneration in primates. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1274–1282, 2017.
TSGDB: a database system for tumor suppressor genes

UNLABELLED A Web-based database system was constructed and implemented that contains 174 tumor suppressor genes. The database homepage was created to accommodate these genes in a pull-down window so that each gene can be viewed individually in a separate Web page. Information displayed on each page includes gene name, aliases, source organism, chromosome location, expression cells/tissues, gene structure, protein size, gene functions and major reference sources. Queries to the database can be conducted through a user-friendly interface, and query results are returned in the HTML format on dynamically generated web pages. AVAILABILITY The database is available at http://www.cise. ufl.edu/~yy1/HTML-TSGDB/Homepage.html (data files also at http://www.patcar.org/Databases/Tumor_Suppressor_Genes)
Bioavailability of repaglinide, a novel antidiabetic agent, administered orally in tablet or solution form or intravenously in healthy male volunteers.

OBJECTIVE Repaglinide is a novel prandial glucose regulator (PGR) for the treatment of type 2 diabetes. In order to investigate subject variability following oral administration of repaglinide, and to determine the relative and absolute bioavailabilities of repaglinide following oral or intravenous administration, two single-centre, open-label, randomized, crossover clinical studies were conducted. SUBJECTS AND METHODS Study 1 was conducted in 24 healthy male subjects (aged 18 to 49 years), who received repaglinide 2 mg, as either tablet or oral solution, twice each on 4 separate occasions at least 7 days apart. Study 2 was conducted in 12 healthy male subjects (aged 18 to 45 years), who received repaglinide 2 mg, either as a tablet or as an intravenous infusion over 15 minutes, once each on 2 separate occasions, with a washout period of 7-10 days. RESULTS In study 1 there was no significant difference between administration of repaglinide 2 mg, in either tablet or oral solution form with regard to intrasubject variation in AUC and Cmax. However, the intrasubject variation in t(max) and mean residence time (MRT) was significantly (p = 0.001) larger for the tablets than for the oral solution. Intersubject variation (CV) in AUC ranged from 44.7% to 62.1% after oral administration. The relative bioavailability of repaglinide (AUC(tablet)/AUC(oral solution)) was 110% (95% CI, 103%-117%). In study 2 the absolute bioavailability of repaglinide administered as a tablet was 62.5% (95% CI, 49.2%-79.5%) relative to an intravenous infusion of the same dose. CONCLUSION There was no evidence from either study that the tablet formulation led to greater variation in serum profiles of repaglinide. It was concluded that repaglinide is rapidly absorbed and eliminated in healthy subjects when administered orally or intravenously under fasting conditions, and that the total availability of repaglinide is similar in the tablet and oral solution formulations, though that the rate of absorption is slower for the tablet formulation.
Virtual base station election for wireless sensor networks

In a classical wireless sensor network, a base station is often present to ensure efficient data collection. Endowed with typical hardware feature, especially with high energy level and good stockpiling capabilities, the base station completes the architecture as a required component for a wide range of applications. However, there are some projects where base station deployment should be avoided without reducing network efficiency. Thus, in a cold chain supervision project, itŠs not necessary to add base station to a wireless sensors network deployed inside a food or a medical truck. In this manner, it is a low-budget sensors network deployment. Moreover, such applications have to replicate data across all nodes and to maintain same information as well. In this paper, we propose databases updating model for homogeneous wireless sensors network deployed in a food truck without any base station. In this model, Virtual Base Station (VBS) is the node which is elected to act as classical base station during a specific period of time. Virtual Base Station (VBS) electionŠs algorithm is based on the remaining energy for each node and latest Virtual Bases Station (VBS) to reduce overall energy spent by network. Simulation results (using MATLAB) show that VBS model introduces very low overhead with respect to the classical network with permanent Base Station (BS).
Under-the-Barrier Model: An Extension of the Top-of-the-Barrier Model to Efficiently and Accurately Simulate Ultrascaled Nanowire Transistors

In this paper, we present a computationally efficient full-band method to determine the current characteristics of circular, gate-all-around nanowire (NW) FETs in the sub-10-nm regime. The well-established top-of-the-barrier model is extended to consider intraband tunneling through the Wentzel-Kramers-Brillouin approximation. The required electrostatic potential is obtained using a parabolic approximation for its radial component, thus reducing Poisson equation to an 1-D problem and the computational burden by several orders of magnitude. After validating the model with 3-D, full-band, atomistic quantum transport simulations, the properties of Si, Ge, and InAs NW FETs are studied as function of their diameter and gate length. It is found that below 10-nm gate lengths Si <;110> NW transistors outperform Ge <;100>, independently from their diameter. On the other hand, InAs <;100> wires with diameters below 6 nm exhibit higher ON-currents than their Si counterparts.
Multi-trap energy states in GaN HEMTs: Characterization and modeling

In this work, presence of multi-trap energy (MTE) levels in the GaN energy bandgap of AlGaN/GaN HEMT is studied based on conductance method as well as temperature-dependent current transient measurements. Using conductance method, it is observed that the MTE model shows a better fit with the measurement data as compared to the single-trap energy (STE) model. Temperature-dependent current transient analysis under fully ON-state stress conditions has also confirmed the presence of distribution of trap energy states in the GaN energy bandgap. The DC trap model is extended to capture the effect of MTE levels. For STE level, the emission-time constant factor saturates very quickly with increasing drain voltage. However, with MTE levels, the time-constant factor continues to increase and saturates at higher drain bias, exhibiting a similar trend as observed in current transient analysis under ON-state stress measurements. The DC trap model with MTE level fit nicely with the numerical simulation data, thus, justifying the physics-based model.
Brief Intervention for Co-Occurring Anxiety and Depression in Primary Care: A Pilot Study

Objective: The purpose of this study was to evaluate the effectiveness of a brief cognitive-behavioral intervention for co-occurring anxiety and depression in primary care patients. Method: Participants in this study were 35 veterans seeking care from a VA primary care clinic. Patients were selected for inclusion in this study based on mild to moderate levels of self-reported symptoms of anxiety and depression. Participants received four weekly sessions of cognitive behavioral intervention for their symptoms. The effectiveness of this intervention was compared with the passage of time alone. Measured outcomes included symptoms of anxiety and depression and quality of life. Results: Statistical testing demonstrated that the intervention led to significant reductions in depression and anxiety and improved role functioning. These changes were maintained except for some return of anxiety over a one-month follow-up period following the end of treatment. Conclusions: This study shows that primary care patients with co-occurring anxiety and depression can be successfully treated with a brief cognitive-behavioral intervention. It is also a test of a flexible treatment approach, whereby the patient and clinician together select the focus of the intervention. Limitations of this pilot work, including patient attrition, are discussed. Further research will be necessary to refine the intervention for primary care patients and to test its effectiveness.