Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal and Spatial Expression of TGF-b 1 in the Early Phase of Patellar Tendon Healing after Application of Platelet Rich Plasma

Background:The aim of this study is to find out the spatial and temporal expression of TGF-b1 during the tendon healing, after application of Platelet Rich Plasma (PRP). Methods: A patellar tendon defect model in rabbits was used for this purpose. 48 skeletally mature New Zealand White rabbits, weighing 3.5 kg, were used for this study. Equal numbers of animals from both groups were sacrificed at 4 different time points (1st, 2nd, 3rd, and 4th week). A full thickness patellar tendon substance in the right limb of each animal was excised from its central portion during the operation. PRP with a gel form was applied and filled the tendon defect in PRP group. No PRP was applied in the tendon defect of controls. Histological sections with hematoxylin-eosin and immunohistochemical sections with an anti-TGF-b1 primary antibody were made for the evaluation of the results. Results: A differentiation of the healing process was observed in the PRP group in comparison with the control group. TGF-b1 expression was detected in various cell populations (inflammatory cells, endothelial cells, macrophages, and tenocytes). Both cytoplasmic and nuclear expressions were present. The larger amounts of immunoexpression were localized in epitenon and in the repair site. PRP group showed stronger and more extensive staining at 1st and 2nd week (P<0.0001), whereas control group showed more extensive staining at the 3rd and 4th week (P<0.0001). Conclusions: Our study demonstrates that locally application of PRP result in an alteration of TGF-b1 expression during the healing of a patellar tendon defect.
Maternal periconceptional exposure to cigarette smoking and congenital limb deficiencies.

BACKGROUND Congenital limb deficiencies (LD)s are characterised by the failure or disruption in formation of limbs or digits. Epidemiological research on maternal exposure to cigarette smoke and LDs is inconclusive. METHODS Data from the National Birth Defects Prevention Study were used to examine LDs and maternal exposure to active or passive cigarette smoke. Mothers of LD case (n = 906) and unaffected control (n = 8352) pregnancies from October 1997 through December 2007 reported on exposure type and quantity. Logistic regression was used to estimate adjusted odds ratio (OR) and 95% confidence interval [95% CI]; interactions with folic acid (FA) intake were tested. RESULTS For any LD, ORs were elevated for active (1.24 [95% CI 1.01, 1.53]), passive (home) (1.28 [95% CI 1.03, 1.59]), and 'active and passive' (1.34 [95% CI 1.05, 1.70]) exposures. The ORs for longitudinal LDs were elevated for passive (home) (1.62 [95% CI 1.14, 2.31]) and 'active and passive' (1.62 [95% CI 1.09, 2.41]) exposures. The OR for pre-axial LDs were elevated for any (1.39 [95% CI 1.01, 1.90]), active (1.53 [95% CI 1.03, 2.29]), passive (home) (1.82 [95% CI 1.23, 2.69]), and 'active and passive' (1.87 [95% CI 1.20, 2.92]) exposures. For lower limbs, ORs were elevated for passive (home) (1.44 [95% CI 1.01, 2.04]) and smoking 15 or more cigarettes/day (2.25 [95% CI 1.27, 3.97]). Interactions showed that ORs for any passive smoke exposure were 0.43 and 0.59 higher in the absence of FA intake for any and terminal transverse LDs. CONCLUSIONS Maternal active smoking and exposure to passive cigarette smoke emerged as a potential teratogen that affects limb and digit formation. FA was not found to mitigate the impact.
COMPARATIVE STUDY OF PULMONARY FUNCTION TESTS IN SMOKERS AND NON SMOKERS

Smoking is one of the most harmful and addictive habits which is wide spread all over the world. Deleterious effects of tobacco are seen on all body systems but most markedly on respiratory and cardiovascular systems. Nicotine present in tobacco is the most dangerous of all psychoactive substances which is harmful to human race. Approximately 40% of cigarette smokers will die prematurely due to cigarette smoking unless they are able to quit. The present study was conducted on human male subjects comprising of 75 apparently healthy smokers of ages ranging from 20-25, 30-35 & 40-45 years and an equal number of healthy non smokers of the same age groups. Statistical analysis was carried out using standard deviation and chi-square from which ‘p’ value is derived. The FVC, FEV1, PEFR & FVC25-75% are effort dependent and are decreased uniformly in smokers when compared with non-smokers. This suggests smoking effects respiratory system in a significant way. In this study there is decrease in PFT values with increasing age which suggests natural respiratory changes with age. Smokers showed much more lower values as compared to nonsmokers which reflects that smoking has a definite bad impact on the natural age related changes of respiratory system .
Overexpressed tryptophanyl-tRNA synthetase, an angiostatic protein, enhances oral cancer cell invasiveness

Oral squamous cell carcinoma (OSCC) is one of the most common neoplasms worldwide. Previously, we identified the angiostatic agent tryptophanyl-tRNA synthetase (TrpRS) as a dysregulated protein in OSCC based on a proteomics approach. Herein, we show that TrpRS is overexpressed in OSCC tissues (139/146, 95.2%) compared with adjacent normal tissues and that TrpRS expression positively correlates with tumor stage, overall TNM stage, perineural invasion and tumor depth. Importantly, the TrpRS levels were significantly higher in tumor cells from metastatic lymph nodes than in corresponding primary tumor cells. TrpRS knockdown or treatment with conditioned media obtained from TrpRS-knockdown cells significantly reduced oral cancer cell viability and invasiveness. TrpRS overexpression promoted cell migration and invasion. In addition, the extracellular addition of TrpRS rescued the invasion ability of TrpRS-knockdown cells. Subcellular fractionation and immunofluorescence staining further revealed that TrpRS was distributed on the cell surface, suggesting that secreted TrpRS promotes OSCC progression via an extrinsic pathway. Collectively, our results demonstrated the clinical significance and a novel role of TrpRS in OSCC.
Localization of Kv2.2 protein in Xenopus laevis embryos and tadpoles

Voltage‐gated potassium (Kv) channels sculpt neuronal excitability and play important developmental roles. Kv channels consist of pore‐forming α‐ and auxiliary subunits. For many Kv α‐subunits, existing mRNA probes and antibodies have allowed analysis of expression patterns, typically during adult stages. Here, we focus on the Kv2.2 α‐subunit, for which the mRNA shows broad expression in the embryo and adult. A lack of suitable antibodies, however, has hindered detailed analysis of Kv2.2 protein localization, especially during development. We developed an antibody that specifically recognizes Kv2.2 protein in Xenopus laevis, a vertebrate well suited for study of early developmental stages. The Kv2.2 antibody recognized heterologously expressed Kv2.2 but not the closely related Kv2.1 protein. Immunodetection of the protein showed its presence at St 32 in ventrolateral regions of the hindbrain and spinal cord. At later stages, several sensory tissues (retina, otic, and olfactory epithelia) also expressed Kv2.2 protein. As development progressed in the central nervous system, Kv2.2 protein distribution expanded in close association with the cytoskeletal marker α‐tubulin, consistent with growth of neuronal tracts. We analyzed the subcellular distribution of Kv2.2 protein within single cultured neurons. In addition to a surface membrane presence, Kv2.2 protein also resided intracellularly closely associated with α‐tubulin, as in vivo. Furthermore, in contrast to Kv2.1, Kv2.2 protein localized to long, axonal‐like processes, consistent with its in vivo location in tracts. Despite their primary sequence similarity, the contrasting localizations of Kv2.1 and Kv2.2 support different roles for the two during development and neuronal signaling. J. Comp. Neurol. 510:508–524, 2008. © 2008 Wiley‐Liss, Inc.
Climate change impact assessment: Uncertainty modeling with imprecise probability

Hydrologic impacts of climate change are usually assessed by downscaling the General Circulation Model (GCM) output of large-scale climate variables to local-scale hydrologic variables. Such an assessment is characterized by uncertainty resulting from the ensembles of projections generated with multiple GCMs, which is known as intermodel or GCM uncertainty. Ensemble averaging with the assignment of weights to GCMs based on model evaluation is one of the methods to address such uncertainty and is used in the present study for regional-scale impact assessment. GCM outputs of large-scale climate variables are downscaled to subdivisional-scale monsoon rainfall. Weights are assigned to the GCMs on the basis of model performance and model convergence, which are evaluated with the Cumulative Distribution Functions (CDFs) generated from the downscaled GCM output (for both 20th Century [20C3M] and future scenarios) and observed data. Ensemble averaging approach, with the assignment of weights to GCMs, is characterized by the uncertainty caused by partial ignorance, which stems from nonavailability of the outputs of some of the GCMs for a few scenarios (in Intergovernmental Panel on Climate Change [IPCC] data distribution center for Assessment Report 4 [AR4]). This uncertainty is modeled with imprecise probability, i.e., the probability being represented as an interval gray number. Furthermore, the CDF generated with one GCM is entirely different from that with another and therefore the use of multiple GCMs results in a band of CDFs. Representing this band of CDFs with a single valued weighted mean CDF may be misleading. Such a band of CDFs can only be represented with an envelope that contains all the CDFs generated with a number of GCMs. Imprecise CDF represents such an envelope, which not only contains the CDFs generated with all the available GCMs but also to an extent accounts for the uncertainty resulting from the missing GCM output. This concept of imprecise probability is also validated in the present study. The imprecise CDFs of monsoon rainfall are derived for three 30-year time slices, 2020s, 2050s and 2080s, with A1B, A2 and B1 scenarios. The model is demonstrated with the prediction of monsoon rainfall in Orissa meteorological subdivision, which shows a possible decreasing trend in the future.
Performance of network coding for ad hoc networks in realistic simulation scenarios

Network coding has recently emerged as an effective solution for multicast and broadcast communications in ad hoc networks. We focus on broadcast traffic and design a network coding-based scheme that we compare against simpler solutions, by using the network simulator ns-2. Indeed, while often the benefits of network coding have been shown via theoretical analysis or in simplified simulation scenarios, our aim is to assess the performance of network coding in ad hoc networks when a realistic MAC protocol is considered. Our results show that the performance of network coding for traffic broadcasting strongly depends on the network node density and on the generation size. In particular, network coding leads to significant gains in terms of end-to-end packet loss probability and protocol overhead only when the average number of neighbors per node is higher than 12.
"The People of Tuscany and Their Families in the Fifteenth Century: Medieyal or Mediterranean?"

western Europe working in the field of demographic and family history might well think that those in this small band of specialists whose field of enquiry is the Mediterranean region have been disproportionately endowed with all the best source materials. For instance, the notarial registers of many southern European towns permit a style of investigation into family relationships and kinship systems that can prove particularly illuminating (Hughes, 1974, 1975, 1977, 1978; Cohn, 1978). There is hardly a medievalist living who must not despair of ever finding a document equivalent to Le Registre d’Inquisition de Jacques Fournier concerning the southwestern French village of Montaillou and its environs that Le Roy Ladurie (1975) has brilliantly turned into
Vitamin B-6 restriction reduces the production of hydrogen sulfide and its biomarkers by the transsulfuration pathway in cultured human hepatoma cells.

BACKGROUND Pyridoxal 5'-phosphate (PLP) functions as a coenzyme in many cellular processes including one-carbon metabolism and the interconversion and catabolism of amino acids. PLP-dependent enzymes, cystathionine β-synthase and cystathionine γ-lyase, function in transsulfuration but also have been implicated in the production of the endogenous gaseous signaling molecule hydrogen sulfide (H2S) concurrent with the formation of the biomarkers lanthionine and homolanthionine. OBJECTIVE Our objective was to determine if H2S production and concurrent biomarker production is affected by vitamin B-6 restriction in a cell culture model. METHODS We used cultured human hepatoma cells and evaluated static intracellular profiles of amino acids and in vivo kinetics of H2S biomarker formation. Cells were cultured for 6 wk in media containing concentrations of pyridoxal that represented severe vitamin B-6 deficiency (15 nmol/L pyridoxal), marginal deficiency (56 nmol/L pyridoxal), adequacy (210 nmol/L pyridoxal), and standard medium formulation providing a supraphysiologic pyridoxal concentration (1800 nmol/L pyridoxal). RESULTS Intracellular concentrations of lanthionine and homolanthionine in cells cultured at 15 nmol/L pyridoxal were 50% lower (P < 0.002) and 47% lower (P < 0.0255), respectively, than observed in cells cultured at 1800 nmol/L pyridoxal. Extracellular homocysteine and cysteine were 58% and 46% higher, respectively, in severely deficient cells than in adequate cells (P < 0.002). Fractional synthesis rates of lanthionine (P < 0.01) and homolanthionine (P < 0.006) were lower at 15 and 56 nmol/L pyridoxal than at both higher pyridoxal concentrations. The rate of homocysteine remethylation and the fractional rate of homocysteine production from methionine were not affected by vitamin B-6 restriction. In vitro studies of cell lysates using direct measurement of H2S also had a reduced extent of H2S production in the 2 lower vitamin B-6 conditions. CONCLUSION In view of the physiologic roles of H2S, these results suggest a mechanism that may be involved in the association between human vitamin B-6 inadequacy and its effects on human health.
Non-Native R1 Substitution in the S4 Domain Uniquely Alters Kv4.3 Channel Gating

The S4 transmembrane domain in Shaker (Kv1) voltage-sensitive potassium channels has four basic residues (R1–R4) that are responsible for carrying the majority of gating charge. In Kv4 channels, however, R1 is replaced by a neutral valine at position 287. Among other differences, Kv4 channels display prominent closed state inactivation, a mechanism which is minimal in Shaker. To determine if the absence of R1 is responsible for important variation in gating characteristics between the two channel types, we introduced the V287R mutant into Kv4.3 and analyzed its effects on several voltage sensitive gating transitions. We found that the mutant increased the voltage sensitivity of steady-state activation and altered the kinetics of activation and deactivation processes. Although the kinetics of macroscopic inactivation were minimally affected, the characteristics of closed-state inactivation and recovery from open and closed inactivated states were significantly altered. The absence of R1 can only partially account for differences in the effective voltage sensitivity of gating between Shaker and Kv4.3. These results suggest that the S4 domain serves an important functional role in Kv4 channel activation and deactivation processes, and also those of closed-state inactivation and recovery.
Measuring Privacy and Utility in Privacy‐Preserving Visualization

In previous work, we proposed a technique for preserving the privacy of quasi‐identifiers in sensitive data when visualized using parallel coordinates. This paper builds on that work by introducing a number of metrics that can be used to assess both the level of privacy and the amount of utility that can be gained from the resulting visualizations. We also generalize our approach beyond parallel coordinates to scatter plots and other visualization techniques. Privacy preservation generally entails a trade‐off between privacy and utility: the more the data are protected, the less useful the visualization. Using a visually‐oriented approach, we can provide a higher amount of utility than directly applying data anonymization techniques used in data mining. To demonstrate this, we use the visual uncertainty framework for systematically defining metrics based on cluster artifacts and information theoretic principles. In a case study, we demonstrate the effectiveness of our technique as compared to standard data‐based clustering in the context of privacy‐preserving visualization.
Identification of mutagens in freshwater sediments by the Ames‐fluctuation assay using nitroreductase and acetyltransferase overproducing test strains

Extracts of sediments from an area of concern in the Elbe river basins (Spittelwasser creek) were analyzed with the Ames‐fluctuation test and in parallel with gas chromatography/mass spectrometry for compound identification. The standard test strains TA 98 and TA 100 showed mutagenicity mainly in medium‐polar fractions of the sediment extracts. PAHs contribute to the overall mutagenic potential of the sample. Especially, cyclopenta[c,d]pyrene that was previously not defined as a priority hazardous substance has to be considered as well. The addition of metabolically competent test strains, which overexpress nitroreductase and acetyltransferase (e.g., YG1041 and YG1042) to the test battery, increased significantly the sensitivity of the Ames test for medium polar to polar genotoxins. The increased mutagenicity that was found in these bacterial strains indicates the presence of nitroarenes and/or aromatic amines. In fact, a number of heterocyclic and nitrogen‐substituted aromatic compounds were identified in the sediments of the Spittelwasser creek of which methyl parathion, 1‐naphthylamine, and N‐phenyl‐2‐naphthylamine are mutagenic. Environ. Mol. Mutagen. , 2011. © 2010 Wiley‐Liss, Inc.
CHADS(2) score is predictive of left atrial thrombus on precardioversion transesophageal echocardiography in atrial fibrillation.

OBJECTIVE The goals of this study were to determine: 1) if the CHADS(2) score correlates with left atrial (LA) or left atrial appendage (LAA) thrombus on pre-cardioversion transesophageal echocardiography (TEE) in nonvalvular atrial fibrillation (NVAF); and 2) what, if any, components of the CHADS(2) score are most important in predicting LA/LAA thrombus. BACKGROUND It is unknown if CHADS(2) score, a marker of thromboembolic risk in NVAF, accurately predicts LA/LAA thrombus on pre-cardioversion TEE. METHODS We retrospectively studied patients undergoing precardioversion TEE for NVAF at a tertiary hospital. TEE reports were reviewed for presence of LA/LAA thrombus. Using medical records and an ICD-9 coding database, a CHADS(2) score was derived, and the association between CHADS(2) and thrombus was evaluated with Mantel-Haenszel Chi-Square. The relation between the singular components of CHADS(2) and thrombus were analyzed using Pearson's Chi-Square. RESULTS In 643 consecutive patients undergoing pre-cardioversion TEE, LA/LAA thrombus was identified in 46 (7.2 %). A strong association was present between CHADS(2)score and LA/LAA thrombus (p = 0.0005). No thrombi were identified in patients with CHADS(2) = 0. Among 46 patients with thrombus, all (100%) had CHF. Of the singular components, CHF was the only factor independently associated with thrombus (p < 0.0001). CONCLUSIONS In non-valvular atrial fibrillation, CHADS(2) is strongly associated with LA thrombus on TEE. Our findings suggest pre-cardioversion TEE may be unnecessary if the CHADS(2) score = 0. Of the components of the CHADS(2) score, CHF was the only independently associated risk factor which correlated with LA/LAA thrombus.
A semi-phenomenological model to predict the acoustic behavior of fully and partially reticulated polyurethane foams

This paper proposes simple semi-phenomenological models to predict the sound absorption efficiency of highly porous polyurethane foams from microstructure characterization. In a previous paper [J. Appl. Phys. 110, 064901 (2011)], the authors presented a 3-parameter semi-phenomenological model linking the microstructure properties of fully and partially reticulated isotropic polyurethane foams (i.e., strut length l, strut thickness t, and reticulation rate Rw) to the macroscopic non-acoustic parameters involved in the classical Johnson-Champoux-Allard model (i.e., porosity ϕ, airflow resistivity σ, tortuosity α∝, viscous Λ, and thermal Λ′ characteristic lengths). The model was based on existing scaling laws, validated for fully reticulated polyurethane foams, and improved using both geometrical and empirical approaches to account for the presence of membrane closing the pores. This 3-parameter model is applied to six polyurethane foams in this paper and is found highly sensitive to the microstructure chara.
CD4 T Follicular Helper and Regulatory Cell Dynamics and Function in HIV Infection

T follicular helper cells (TFH) are a specialized subset of CD4 T cells that reside in B cell follicles and promote B cell maturation into plasma cells and long-lived memory B cells. During chronic infection prior to the development of AIDS, HIV-1 (HIV) replication is largely concentrated in TFH. Paradoxically, TFH numbers are increased in early and midstages of disease, thereby promoting HIV replication and disease progression. Despite increased TFH numbers, numerous defects in humoral immunity are detected in HIV-infected individuals, including dysregulation of B cell maturation, impaired somatic hypermutation, and low quality of antibody production despite hypergammaglobulinemia. Clinically, these defects are manifested by increased vulnerability to bacterial infections and impaired vaccine responses, neither of which is fully reversed by antiretroviral therapy (ART). Deficits in TFH function, including reduced HIV-specific IL-21 production and low levels of co-stimulatory receptor expression, have been linked to these immune impairments. Impairments in TFH likely contribute as well to the ability of HIV to persist and evade humoral immunity, particularly the inability to develop broadly neutralizing antibodies. In addition to direct infection of TFH, other mechanisms that have been linked to TFH deficits in HIV infection include upregulation of PD-L1 on germinal center B cells and augmented follicular regulatory T cell responses. Challenges to development of strategies to enhance TFH function in HIV infection include lack of an established phenotype for memory TFH as well as limited understanding of the relationship between peripheral TFH and lymphoid tissue TFH. Interventions to augment TFH function in HIV-infected individuals could enhance immune reconstitution during ART and potentially augment cure strategies.