Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a system for individual feeding of baboons maintained in an outdoor group social environment

Abstract: We developed a system that allows individual feeding of adult baboons, 8–15 years of age, maintained in an outdoor group social environment. The purpose of the system is to allow careful monitoring and control of individual diet. Baboons were housed in two group cages, 16 females and a single male in one and 12 females and a single male in the other. Baboons exited the group cage once daily and passed along a chute and over a scale into individual cages where they received their individual diets. Food intake was monitored during their 2‐hour stay in the individual cages. Baboons rapidly learned to use this system. Food intake and weight were stable within 20 days. Food consumed decreased during the period of sexual receptivity. The maintenance of the group social environment allowed observations on the group's dominance structure and the relationship of dominance to food consumption. Speed of food access in the group cage was related to dominance. Dominance was not related to food consumed in individual cages. The system permits study of many variables related to behavior and food intake while still retaining critical social interactions.
Identifying stone composition using infrared analysis of filtered urine after ureteroscopic lithotripsy.

BACKGROUND AND PURPOSE With the development of small-caliber ureteroscopes and lithotripsy devices, it is now possible to perform intracorporeal stone fragmentation without dilatation of the ureteral orifice. Ureteral stones are typically fragmented into small particles that can be difficult to retrieve for stone analysis. Infrared spectroscopy (IRS) of the precipitate from urine after intracorporeal lithotripsy represents a method for obtaining stone analysis. PATIENTS AND METHODS A total of 69 patients underwent ureteroscopic lithotripsy with the holmium laser or the electrohydraulic probe for stones in the ureter (N = 65) or kidney (N = 4). Each patient's bladder was then drained and the urine filtered. The resulting precipitate was analyzed using IRS. RESULTS The amount of material for analysis was < or =1 mg in 56 patients (82%). Stone composition was positively identified in 44 patients (64%). Material suitable for analysis was recovered from 73% of patients when the bladder was drained with a cystoscope sheath compared with 43% when a urethral catheter was used (P = 0.03). There was no significant difference in pretreatment stone size in the patients who had a positive v a negative result (11.7 mm v 10.9 mm; P = 0.06). Similarly, the stone location was not significantly related to the likelihood of positive analysis (P = 0.29). CONCLUSION Straining the urine after ureteroscopic intracorporeal lithotripsy and analyzing the precipitate with IRS is able to identify stone composition in the majority of patients. This method is especially useful in the setting of holmium laser lithotripsy, in which the majority of the stone is converted to spontaneously passable particles.
Enhanced production of avermectin by deletion of type III polyketide synthases biosynthetic cluster rpp in Streptomyces avermitilis

The rpp biosynthetic gene cluster (sav7130–7131) in Streptomyces avermitilis contains a type III polyketide synthases (PKSs) and a cytochrome P450 and was reportedly involved in producing a diffusible brown pigment. Since the same precursor malonyl‐CoA was used as substrate for the type I PKSs and type III PKSs, there might be a competition for precursor between rpp gene cluster and avermectin biosynthetic cluster. In this work, rpp biosynthetic gene cluster deletion mutants were constructed to improve avermectin production. In an industrial strain AV‐LP, rpp deletion improved avermectin production from 1024 to 1262 mg l−1 without any effect on the cell growth. In the same way, the production of an industrial overproducer increased from 3582 to 4450 mg l−1. Transcriptional analysis suggested that the deletion of rpp gene cluster stimulated transcription of aveR, leading to increased transcription of biosynthetic gene aveA1 and a consequent increase in avermectin production.
Trophic‐level dependent effects on CO2 emissions from experimental stream ecosystems

Concern over accelerating rates of species invasions and losses have initiated investigations into how local and global changes to predator abundance mediate trophic cascades that influence CO2 fluxes of aquatic ecosystems. However, to date, no studies have investigated how species additions or losses at other consumer trophic levels influence the CO2 flux of aquatic ecosystems. In this study, we added a large predatory stonefly, detritivorous stonefly, or grazer tadpole to experimental stream food webs and over a 70‐day period quantified their effects on community composition, leaf litter decomposition, chlorophyll‐a concentrations, and stream CO2 emissions. In general, streams where the large grazer or large detritivore were added showed no change in total invertebrate biomass, leaf litter loss, chlorophyll‐a concentrations, or stream CO2 emissions compared with controls; although we did observe a spike in CO2 emissions in the large grazer treatment following a substantial reduction in chlorophyll‐a concentrations on day 28. However, the large grazer and large detritivore altered the community composition of streams by reducing the densities of other grazer and detritivore taxa, respectively, compared with controls. Conversely, the addition of the large predator created trophic cascades that reduced total invertebrate biomass and increased primary producer biomass. The cascading effects of the predator additions on the food web ultimately led to decreased CO2 emissions from stream channels by up to 95%. Our results suggest that stream ecosystem processes were more influenced by changes in large predator abundance than large grazer or detritivore abundance, because of a lack of functionally similar large predators. Our study demonstrates that the presence/absence of species with unique functional roles may have consequences for the exchange of CO2 between the ecosystem and the atmosphere.
Hepatitis C virus genotype 3 and the risk of severe liver disease in a large population of drug users in France

Although risk factors for cirrhosis in chronic hepatitis C virus (HCV) infection have been identified, the role of HCV‐genotype 3 remains controversial, and limited data are available in drug users. The aim of the study was to assess risk factors for severe liver disease (cirrhosis/hepatocellular carcinoma) in HCV‐infected drug users between 2001 and 2007 in France. Patients who reported drug use and who had been referred for HCV infection to hepatology centers from a national surveillance system were identified. The severity of liver disease was assessed clinically and histologically (Metavir score). Factors associated with severe liver disease were analyzed after estimating missing values by multiple imputation (MI). Of the 4,065 drug users naive to anti‐HCV treatment who were referred to the 26 participating centers, 8.0% had severe liver disease, 25.7% were infected with HCV‐genotype 3. Factors associated independently with an increased risk of severe liver disease were HCV‐genotype 3 (adjusted odds ratio, multiple imputation (aORMI) = 1.6, [95% confidence interval, 95% CI: 1.2–2.1]), HIV infection (aORMI = 1.8, [1.2–2.8]), male sex (aORMI = 2.0, [1.4–2.8]), age over 40 years (aORMI = 2.1, [1.6–2.9]), history of excessive alcohol consumption (aORMI = 2.8, [2.1–3.7]), and duration of infection ≥18 years (aORMI = 2.9, [2.0–4.3]). This analysis shows that HCV‐genotype 3 is associated with severe liver disease in drug users, independently of age, sex, duration of infection, alcohol consumption, and co‐infection with HIV. These results are in favor of earlier treatment for drug users infected with HCV‐ genotype 3 and confirm the need for concomitant care for excessive alcohol consumption. J. Med. Virol. 82:1647–1654, 2010. 2010 Wiley‐Liss, Inc.
Modeling pigment contributions to spectral reflection of apple fruit

A simple approach for spectral reconstruction of spectral reflection by whole apple fruit is described. It is shown that an approximation to the reflection spectrum can be obtained by making a simple assumption on the shape of the featureless scattering and using known spectral properties of the following pigment pools: (i) thylakoid-bound chlorophylls and carotenoids, (ii) cuticular/vacuolar phenolics, (iii) extrathylakoid chloroplasts/chromoplasts carotenoids, and (iv) vacuolar anthocyanins. The in vivo spectra of individual pigment pools estimated in bleaching experiments or as a difference between fruit with high and low pigment content are presented. In most cases simulations based on a linear combination of spectra proved to be effective, but fruit with high chlorophyll content necessitated the use of a non-linear model. The models succeeded in simulating reflection spectra of fruit widely differing in pigment content and composition with relative error lower than ±4% over the visible range. The estimated relative contributions by the pigment pools into total reflection were found to be sensitive indicators of apple fruit ripening and could be useful in evaluating the light screening efficacy by flavonoids and carotenoids under stress conditions.
Palliative medicine consultation impacts DNR designation and length of stay for terminal medical MICU patients

Abstract Objective: The purpose of this study was to assess the impact of a palliative medicine consultation on medical intensive care unit (MICU) and hospital length of stay, Do Not Resuscitate (DNR) designation, and location of death for MICU patients who died during hospitalization. Method: A comparison of two retrospective cohorts in a 17-bed MICU in a tertiary care university-affiliated hospital was conducted. Patients admitted to the MICU between January 1, 2003 and June 30, 2004 (N = 515) were compared to MICU patients who had had a palliative medicine consultation between January 1, 2005 and June 1, 2009 (N = 693). To control for disease severity, only patients in both cohorts who died during their hospitalization were considered for this study. Results: Palliative medicine consultation reduced time until death during the entire hospitalization (log-rank test, p < 0.01). Time from MICU admission until death was also reduced (log-rank test, p < 0.01), further demonstrating the impact of the palliative care consultation on the duration of dying for hospitalized patients. The intervention group contained a significantly higher percentage of patients with a DNR designation at death than did the control group (86% vs. 68%, χ2 test, p < 0.0001). Significance of results: Palliative medicine consultation is associated with an increased rate of DNR designation and reduced time until death. Patients in the intervention group were also more likely to die outside the MICU as compared to controls in the usual care group.
Application of lag‐time into exposure definitions to control for protopathic bias

To control for protopathic bias, some studies have incorporated the concept of lag‐time into their exposure definition (time period before the index date that was not considered in assessing exposure). The objective of this study was to introduce a procedure to identify the best lag‐time to be applied in studies where control for protopathic bias is required.
Quantitative Multiparametric MRI Features and PTEN Expression of Peripheral Zone Prostate Cancer: A Pilot Study.

OBJECTIVE The objective of our study was to investigate associations between quantitative image features of multiparametric MRI of the prostate and PTEN expression of peripheral zone prostate cancer. MATERIALS AND METHODS A total of 45 peripheral zone cancer foci from 30 patients who had undergone multiparametric prostate MRI before prostatectomy were identified by a genitourinary pathologist and a radiologist who reviewed histologic findings and MR images. Histologic sections of cancer foci underwent immunohistochemical analysis and were scored according to the percentage of tumor-positive cells expressing PTEN as negative (0-20%), mixed (20-80%), or positive (80-100%). Average and 10th percentile apparent diffusion coefficient (ADC) values, skewness of T2-weighted signal intensity histogram, and quantitative perfusion parameters (i.e., forward volume transfer constant [K(trans)], extravascular extracellular volume fraction [ve], and reverse reflux rate constant between the extracellular space and plasma [k(ep)]) from the Tofts model were calculated for each cancer focus. Associations between the quantitative image features and PTEN expression were analyzed with the Spearman rank correlation coefficient (r). RESULTS Analysis of the 45 cancer foci revealed that 21 (47%) were PTEN-positive, 12 (27%) were PTEN-negative, and 12 (27%) were mixed. There was a weak but significant negative correlation between Gleason score and PTEN expression (r = -0.30, p = 0.04) and between k(ep) and PTEN expression (r = -0.35, p = 0.02). There was no significant correlation between other multiparametric MRI features and PTEN expression. CONCLUSION This preliminary study of radiogenomics of peripheral zone prostate cancer revealed weak-but significant-associations between the quantitative dynamic contrast-enhanced MRI feature k(ep) and Gleason score with PTEN expression. These findings warrant further investigation and validation with the aim of using multiparametric MRI to improve risk assessment of patients with prostate cancer.
Control strategy of PV inverter under unbalanced grid voltage sag

The presence of unbalanced voltage sag in grid actual operation gives rise to the output power fluctuation of PV inverter, the increasing of output current harmonics and unbalanced current. The calculation of the output current reference is a key technology in the control of PV inverter and has important influence on the output of the PV inverter under unbalanced grid voltage. Base on the instantaneous power theory, this paper proposed a calculation method of PV inverter current reference under unbalanced voltage sag. The proposed method will not bring harmonic current problems, with the benefits of selectively elimination of active power fluctuations, reactive power fluctuations or negative sequence component. In addition, the inverter output active and reactive power fluctuation can be flexibly adjusted by changing the value of the variable given in the proposed calculation method. Theoretical analysis and simulation results verify the validity of the proposed calculation method of current reference.
A national record linkage to study acute myocardial infarction incidence and case fatality in Sweden.

BACKGROUND During the last decades substantial temporal changes, as well as population differences, in coronary heart disease mortality have occurred in Sweden. There is little information to what extent these changes and differences also apply to myocardial infarction incidence. The aim of this paper was to describe the methods used to identify cases in a recently developed National Acute Myocardial Infarction Register in Sweden, and to present estimates of incidence and case fatality in Sweden. MATERIAL AND METHODS Incident cases of acute myocardial infarction (AMI) were identified by record linkage of routinely collected data on hospital discharges and deaths. Case fatality within 28 days was ascertained by linkage of incident cases to the National Cause of Death Register. RESULTS About 40 000 new cases of AMI per year were recorded in Sweden during 1987-1995. Well-known differences in incidence with regard to age and gender were observed, as well as a decline in incidence between 1987 and 1995. A similar case fatality was seen in men and women aged 30-89 among hospitalized cases. When fatal cases outside hospital were also considered the case fatality was somewhat higher in men. Examination of medical records for a national sample of ischaemic heart disease patients suggested a high sensitivity (94%) and a high positive predictive value (86%) for ICD-9 code 410 in hospital discharge data with regard to definite AMI. CONCLUSIONS The National Acute Myocardial Infarction Register offers a new possibility to study the incidence of AMI, as well as case fatality, in Sweden.
Detection of Chlamydia trachomatis in urine specimens from women by ligase chain reaction

The performance of a plasmid-based ligase chain reaction (LCR) with urine specimens was compared with those of cell culture of cervical swabs and enzyme immunoassay with urine specimens for the detection of Chlamydia trachomatis infection in women who had attended a family planning clinic. The prevalence of chlamydial infection determined by LCR was 3.1%. Discrepant results among the three assays were resolved by testing urine by a second LCR assay based on the C. trachomatis chromosomal gene encoding the major outer membrane protein. Sensitivity, specificity, and positive and negative predictive values for the cell cultures were 56.3, 100, 100, and 98.4%, respectively, whereas those for the enzyme immunoassay were 18.8, 100, 100, and 97.1%, respectively, and those for LCR were 87.5, 100, 100, and 99.5%, respectively. LCR thus provides a highly sensitive and specific noninvasive screening method for detecting genital chlamydial infections in women.
Androgen receptor overexpression alters binding dynamics of the receptor to chromatin and chromatin structure

Castration‐resistant prostate cancers (CRPCs) overexpress often androgen receptor (AR). Here, we investigated the effect of AR overexpression on the dynamics of AR loading and RNA polymerase II (RNA Pol II) recruitment to chromatin. Acetylation of histone 3 (AcH3) on lysines 9 and 14 (K9 and K14) was also studied.
Helicobacter pylori Infection Induces Oxidative Stress and Programmed Cell Death in Human Gastric Epithelial Cells

ABSTRACT Helicobacter pylori infection is associated with altered gastric epithelial cell turnover. To evaluate the role of oxidative stress in cell death, gastric epithelial cells were exposed to various strains of H. pylori, inflammatory cytokines, and hydrogen peroxide in the absence or presence of antioxidant agents. Increased intracellular reactive oxygen species (ROS) were detected using a redox-sensitive fluorescent dye, a cytochrome c reduction assay, and measurements of glutathione. Apoptosis was evaluated by detecting DNA fragmentation and caspase activation. Infection with H. pylori or exposure of epithelial cells to hydrogen peroxide resulted in apoptosis and a dose-dependent increase in ROS generation that was enhanced by pretreatment with inflammatory cytokines. Basal levels of ROS were greater in epithelial cells isolated from gastric mucosal biopsy specimens from H. pylori-infected subjects than in cells from uninfected individuals. H. pylori strains bearing the cag pathogenicity island (PAI) induced higher levels of intracellular oxygen metabolites than isogenic cag PAI-deficient mutants. H. pylori infection and hydrogen peroxide exposure resulted in similar patterns of caspase 3 and 8 activation. Antioxidants inhibited both ROS generation and DNA fragmentation by H. pylori. These results indicate that bacterial factors and the host inflammatory response confer oxidative stress to the gastric epithelium during H. pylori infection that may lead to apoptosis.
Fault-tolerant PMU placement using algebraic connectivity of graphs

We consider fault-tolerant Phasor Measurement Unit (PMU) placement aiming to minimize the number of PMUs while maintaining system observability under various contingencies. Conventionally, the optimal number of PMUs in a system is determined based on the system's connectivity matrix under no contingency. This paper considers fault-tolerant PMU placement under single branch failure, using integer programming based methodology. Algebraic connectivity, or Fiedler value, is utilized to identify the worst-case single branch failure in terms of connectivity degradation. The proposed PMU placement accounts for this worst-case and covers a large percentage of other single-branch failures. The resulting placement is compared with that obtained without considering connectivity degradation in terms of the percentages of observable systems during any single branch failure. The proposed PMU placement has increased percentages of fully observable systems in the event of any single branch failure compared to non-contingency based placement, with a reasonable increase in number of PMUs.
Uncovering genes required for neuronal morphology by morphology-based gene trap screening with a revertible retrovirus vector

The molecular mechanisms of neuronal morphology and synaptic vesicle transport have been largely elusive, and only a few of the molecules involved in these processes have been identified. Here, we developed a novel morphology‐based gene trap method, which is theoretically applicable to all cell lines, to easily and rapidly identify the responsible genes. Using this method, we selected several gene‐trapped clones of rat pheochromocytoma PC12 cells, which displayed abnormal morphology and distribution of synaptic vesicle‐like microvesicles (SLMVs). We identified several genes responsible for the phenotypes and analyzed three genes in more detail. The first gene was BTB/POZ domain‐containing protein 9 (Btbd9), which is associated with restless legs syndrome. The second gene was cytokine receptor‐like factor 3 (Crlf3), whose involvement in the nervous system remains unknown. The third gene was single‐stranded DNA‐binding protein 3 (Ssbp3), a gene known to regulate head morphogenesis. These results suggest that Btbd9, Crlf3, and Ssbp3 regulate neuronal morphology and the biogenesis/transport of synaptic vesicles. Because our novel morphology‐based gene trap method is generally applicable, this method is promising for uncovering novel genes involved in the function of interest in any cell lines. —Hashimoto, Y. , Muramatsu, K. , Kunii, M. , Yoshimura, S. , Yamada, M. , Sato, T. , Ishida, Y. , Harada, R. , Harada, A. Uncovering genes required for neuronal morphology by morphology‐based gene trap screening with a revertible retrovirus vector. FASEB J. 26, 4662–4674 (2012). www.fasebj. org