Miracle-dz/UniFAR-FTUs huggingface dataset:
Meiotic induction of the yeast HOP1 gene is controlled by positive and negative regulatory sites

The process of meiosis and sporulation in the yeast Saccharomyces cerevisiae is a highly regulated developmental pathway dependent on genetic as well as nutritional signals. The HOP1 gene, which encodes a component of meiotic chromosomes, is not expressed in mitotically growing cells, but its transcription is induced shortly after yeast cells enter the meiotic pathway. Through a series of deletions and mutations in the HOP1 promoter, we located two regulatory sites that are essential for proper regulation of HOP1. One site, called URS1H, brings about repression of HOP1 in mitotic cells and functions as an activator sequence in cells undergoing meiosis. The second site, which we designated UASH, acts as an activator sequence in meiotic cells and has similarity to the binding site of the mammalian CCAAT/enhancer binding protein (C/EBP). Both sites are required for full meiotic induction of the HOP1 promoter. We conclude that in mitotic yeast cells, the URS1H site maintains the repressed state of the HOP1 promoter, masking the effect of the UASH site. Upon entry into meiosis, repression is lifted, allowing the URS1H and UASH sites to activate high-level transcription.
Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-amplification testing.

BACKGROUND Testing of blood donors for human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) RNA by means of nucleic acid amplification was introduced in the United States as an investigational screening test in mid-1999 to identify donations made during the window period before seroconversion. METHODS We analyzed all antibody-nonreactive donations that were confirmed to be positive for HIV-1 and HCV RNA on nucleic acid-amplification testing of "minipools" (pools of 16 to 24 donations) by the main blood-collection programs in the United States during the first three years of nucleic acid screening. RESULTS Among 37,164,054 units screened, 12 were confirmed to be positive for HIV-1 RNA--or 1 in 3.1 million donations--only 2 of which were detected by HIV-1 p24 antigen testing. For HCV, of 39,721,404 units screened, 170 were confirmed to be positive for HCV RNA, or 1 in 230,000 donations (or 1 in 270,000 on the basis of 139 donations confirmed to be positive for HCV RNA with the use of a more sensitive HCV-antibody test). The respective rates of positive HCV and HIV-1 nucleic acid-amplification tests were 3.3 and 4.1 times as high among first-time donors as among donors who gave blood repeatedly. Follow-up studies of 67 HCV RNA-positive donors demonstrated that seroconversion occurred a median of 35 days after the index donation, followed by a low rate of resolution of viremia; three cases of long-term immunologically silent HCV infection were documented. CONCLUSIONS Minipool nucleic acid-amplification testing has helped prevent the transmission of approximately 5 HIV-1 infections and 56 HCV infections annually and has reduced the residual risk of transfusion-transmitted HIV-1 and HCV to approximately 1 in 2 million blood units.
N‐acetyl‐L‐cysteine enhances fisetin‐induced cytotoxicity via induction of ROS‐independent apoptosis in human colonic cancer cells

Oxidative stress or excessive antioxidant levels‐caused redox imbalance can alter apoptotic responses, and N‐acetyl‐L‐cysteine (NAC) was able to inhibit H2O2‐mediated cell death, but unable to prevent apoptosis induced by other chemicals such as etoposide. We now demonstrate that 10 and 20 mM NAC, non‐toxic concentrations, can enhance fisetin (FIS)‐mediated apoptosis in colon cancer cells COLO205. Compared to treatment with FIS alone, combination treatment with NAC increased the expression of cleaved caspase‐3 and PAPR protein, and produced greater density of DNA ladders. NAC reduced the mitochondrial membrane potential of FIS‐treated COLO205 cells with induction of caspase 9 protein cleavage. DNA ladders induced by FIS + NAC were diminished by adding the caspase 3 inhibitor, DEVD‐FMK, and the caspase 9 inhibitor, YVAD‐FMK. Combinatorial treatment COLO205 cells with NAC and FIS showed potent inhibition on ERK protein phosphorylation, compared with those from FIS or NAC‐treated groups by Western blotting using specific antibodies. Addition of the chemical ERK inhibitors, PD98059 and U0126, significantly inhibited ERK protein phosphorylation, accompanied by induced DNA ladder formation, cleavage of caspase 3 and PARP protein in COLO205 cells. Furthermore, NAC showed an enhancement on a FIS‐related chemical chrysin‐induced apoptosis of COLO205 cells, and NAC sensitization of colon cancer cells to FIS‐induced apoptosis was also identify in colonic cancer cells HCT‐116, HT‐29, and HCT‐15 cells. The evidence to support NAC sensitizing human colon cancer cells to FIS‐induced apoptosis was provided, and application of NAC and FIS as a strategy to treat colonic cancer deserved for further in vivo study. © 2013 Wiley Periodicals, Inc.
Reproductive Factors and Non-Hodgkin Lymphoma Risk in the California Teachers Study

Background Non-Hodgkin lymphoma (NHL) is a malignancy etiologically linked to immunomodulatory exposures and disorders. Endogenous female sex hormones may modify immune function and influence NHL risk. Few studies have examined associations between reproductive factors, which can serve as surrogates for such hormonal exposures, and NHL risk by subtype. Methodology/Principal Findings Women in the California Teachers Study cohort provided detailed data in 1995–1996 on reproductive history. Follow-up through 2007 identified 574 women with incident B-cell NHL. Hazard rate ratios (RR) and 95% confidence intervals (CI) were estimated using Cox proportional hazards models to assess associations between reproductive factors and all B-cell NHL combined, diffuse large B-cell lymphomas, follicular lymphomas, and B-cell chronic lymphocytic leukemias/small lymphocytic lymphomas. Pregnancy was marginally associated with lower risk of B-cell NHL (RR = 0.84, 95% CI = 0.68–1.04). Much of the reduction in risk was observed after one full-term pregnancy relative to nulligravid women (RR = 0.75, 95% CI = 0.54–1.06; P for trend <0.01), particularly for diffuse large B-cell lymphomas (P for trend = 0.13), but not among women who had only incomplete pregnancies. Age at first full-term pregnancy was marginally inversely associated with B-cell NHL risk overall (P for trend = 0.08) and for diffuse large B-cell lymphomas (P for trend = 0.056). Breast feeding was not associated with B-cell NHL risk overall or by subtype. Conclusions Full-term pregnancy and early age at first full-term pregnancy account for most of the observed reduction in B-cell NHL risk associated with gravidity. Pregnancy-related hormonal exposures, including prolonged and high-level exposure to progesterone during a full-term pregnancy may inhibit development of B-cell NHL.
Autonomic Self Healing-Based Load Assessment for Load Division in OKKAM Backbone Cluster

Abstract: Self healing systems are considered as cognation-enabled sub form of fault tolerance system. But our experiments that we report in this paper show that self healing systems can be used for performance optimization, configuration management, access control management and bunch of other functions. The exponential complexity that results from interaction between autonomic systems and users (software and human users) has hindered the deployment and user of intelligent systems for a while now. We show that if that exceptional complexity is converted into self-growing knowledge (policies in our case), can make up for initial development cost of building an intelligent system. In this paper, we report the application of AHSEN (Autonomic Healing-based Self management Engine) to in OKKAM Project infrastructure backbone cluster that mimics the web service based architecture of u-Zone gateway infrastructure. The ‘blind’ load division on per-request bases is not optimal for distributed and performance hungry infrastructure such as OKKAM. The approach adopted assesses the active threads on the virtual machine and does resource estimates for active processes. The availability of a certain server is represented through worker modules at load server. Our simulation results on the OKKAM infrastructure show that the self healing significantly improves the performance and clearly demarcates the logical ambiguities in contemporary designs of self healing infrastructures proposed for large scale computing infrastructures.
Evaluation of Black Tea Polyphenol Extract Against the Retrogradation of Starches from Various Plant Sources

The effects of black tea polyphenol extract (BTPE) on the retrogradation of starches from different plant sources were studied using differential scanning calorimetry (DSC) and X-ray diffraction (XRD). DSC analysis shows that the gelatinization temperature of maize starch and starches from different rice varieties increased with increasing BTPE level. After storage at 4 °C, BTPE at a concentration of 15% markedly retarded the retrogradation of maize starch and starches from different rice varieties. Native maize starch and starches from different rice varieties showed typical A-type X-ray diffraction patterns, while native potato starch showed a typical B-type X-ray diffraction pattern. Adding BTPE significantly affected the crystalline region and intensities of X-ray diffraction peaks of maize and rice starch granules. It is concluded that adding BTPE markedly inhibits the retrogradation of maize starch and starches from different rice varieties, but has no significant influence on the gelatinization and retrogradation characteristics of potato starch.
Unpacking the recommended indicator for concurrent sexual partnerships

Using sexual behaviour survey data, we examine the methodological choice for the time period underlying the UNAIDS Reference Group on Estimates, Modelling, and Projections recommended ‘point prevalence’ indicator for concurrency. The results confirm that 6 months before the interview is a good time point for calculating the recommended indicator, but this retrospective estimate is substantially lower than the estimate of concurrency based on the number of current partnerships. The discrepancy is only partially explained by disproportionate missing data in those with more sexual partners.
Clinical quantitative methods

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A Millimeter-Wave (40–45 GHz) 16-Element Phased-Array Transmitter in 0.18-$\mu$ m SiGe BiCMOS Technology

This paper demonstrates a 16-element phased-array transmitter in a standard 0.18-mum SiGe BiCMOS technology for Q-band satellite applications. The transmitter array is based on the all-RF architecture with 4-bit RF phase shifters and a corporate-feed network. A 1:2 active divider and two 1:8 passive tee-junction dividers constitute the corporate-feed network, and three-dimensional shielded transmission-lines are used for the passive divider to minimize area. All signals are processed differentially inside the chip except for the input and output interfaces. The phased-array transmitter results in a 12.5 dB of average power gain per channel at 42.5 GHz with a 3-dB gain bandwidth of 39.9-45.6 GHz. The RMS gain variation is < 1.3 dB and the RMS phase variation is < for all 4-bit phase states at 35-50 GHz. The measured input and output return losses are < -10 dB at 36.6-50 GHz, and <-10 dB at 37.6-50 GHz, respectively. The measured peak-to-peak group delay variation is plusmn 20 ps at 40-45 GHz. The output P-1dB is -5plusmn1.5 dBm and the maximum saturated output power is - 2.5plusmn1.5 dBm per channel at 42.5 GHz. The transmitter shows <1.8 dB of RMS gain mismatch and < 7deg of RMS phase mismatch between the 16 different channels over all phase states. A - 30 dB worst-case port-to-port coupling is measured between adjacent channels at 30-50 GHz, and the measured RMS gain and phase disturbances due to the inter-channel coupling are < 0.15 dB and < 1deg, respectively, at 35-50 GHz. All measurements are obtained without any on-chip calibration. The chip consumes 720 mA from a 5 V supply voltage and the chip size is 2.6times3. 2 mm2.
THE SPECTRAL ENERGY DISTRIBUTIONS OF RED TWO MICRON ALL SKY SURVEY ACTIVE GALACTIC NUCLEI

We present infrared (IR) to X-ray spectral energy distributions (SEDs) for 44 red active galactic nuclei (AGNs) selected from the Two Micron All Sky Survey (2MASS) survey on the basis of their red J − KS color (>2 mag) and later observed by Chandra. In comparison with optically-, radio-, and X-ray-selected AGNs, their median SEDs are red in the optical and near-IR (NIR) with little/no blue bump. Comparison of the various broadband luminosity ratios shows that the main differences lie at the blue end of the optical and in the NIR to far-IR ratios (when available), with the red 2MASS AGNs being redder than the other samples. It thus seems that NIR color selection isolates the reddest subset of AGNs that can be classified optically. The shape of the SEDs is generally consistent with modest absorption by gas (in the X-ray) and dust (in the optical–IR), as demonstrated by comparing the optical and NIR colors with a reddened median SED and observed optical+NIR to intrinsic X-ray ratios. The levels of obscuration, estimated from X-rays, far-IR, and our detailed optical/NIR color modeling, are all consistent implying NH ⩽ few × 1022 cm−2. We present SED models that show how the AGN optical/NIR colors change due to differing amounts of reddening, AGN to host galaxy ratio, redshift, and scattered light emission, and apply them to the sources in the sample. We find that the 2MASS AGN optical color, B − R, and to a lesser extent the NIR color, J − KS, are strongly affected by reddening, host galaxy emission, redshift, and in few, highly polarized objects also by scattered AGN light (<2% of intrinsic AGN light in the R band is scattered; this contribution becomes significant as the direct AGN light is absorbed). The lack of low equivalent widths in the distribution of the [O iii] λ5007 emission line implies a predominance of inclined objects in the red 2MASS sample. The obscuration/inclination of the AGN allows us to see weaker emission components which are generally swamped by the AGN.
Standard Perioperative Imaging Modalities Are Unreliable in Assessing Articular Congruity of Ankle Fractures

Objectives: To determine the sensitivity, specificity, and interobserver and intraobserver reliabilities of intraoperative fluoroscopy and postoperative plain radiographs (XR) in the assessment of articular congruency after open reduction and internal fixation (ORIF) of ankle fractures involving the tibial plafond. Design: Retrospective cohort. Setting: Academic level 1 trauma center. Patients/Participants: One hundred five patients treated surgically for rotational ankle fractures. Intervention: ORIF. Main Outcome Measurements: Sensitivity, specificity, and interobserver and intraobserver reliabilities of fluoroscopy and plain radiographs when compared with computed tomography imaging. Results: The sensitivities of fluoroscopy and XR were 21% and 36%, respectively. Specificities were 95% (fluoroscopy) and 89% (XR). Fluoroscopy interobserver reliability was &kgr; = 0.15, and mean intraobserver reliability was &kgr; = 0.32. XR interobserver and mean intraobserver reliabilities were &kgr; = 0.30 and &kgr; = 0.59. Conclusions: Although results show acceptable specificity, the reliability and sensitivity of both intraoperative fluoroscopy and postoperative XR in the assessment of ankle articular congruency are low. This calls into question available literature correlating clinical results with articular reduction. During ORIF of an intra-articular ankle fracture, surgeons should be highly critical of fluoroscopic imaging that seems adequately reduced and direct visualization of the articular surface should be used as a reduction aid if possible. Furthermore, in the postoperative period, axial imaging may be warranted in patients who have poor clinical outcomes despite apparent anatomic articular reduction to evaluate for occult joint incongruence.
A rapid, semi-automated method for detection of Galbeta1-4GlcNAc alpha2,6-sialyltransferase (EC 2.4.99.1) activity using the lectin Sambucus nigra agglutinin.

Sialyltransferase activity has traditionally been studied by determining the rate at which the enzyme transfers a labeled donor sugar to an acceptor substrate. These types of assays can be difficult to quantitate, and the separation of untransfered donor sugar from the sialylated acceptor is time-consuming. The biosensor-based method described here is both rapid and semi-automated. The NeuAc-alpha2-6Gal-R-specific lectin Sambucus nigra agglutinin (SNA) immobilized to the carboxymethyl dextran surface of a BIAcore sensor chip was used to detect and measure the formation of the NeuAc-alpha2-6Gal-R moieties. The sialyltransferase assays were carried out using modified protocols based on the method described in Rearick, J.I. , Sadler, J.E. , Paulson, J.C. , and Hill, R.L. (1979) Enzymatic characterization of betaD-galactoside alpha2-3 sialyltransferase from porcine submaxillary gland. J. Biol. Chem., 254, 4444-4451. The complete assay mixture was simply diluted before injection into the instrument. All injections were performed automatically using the robotics of the BIAcore instrument. Using this technique it is possible to detect product from 0.4 microU of commercial Galbeta1-4GlcNAc alpha2,6-sialyltransferase (EC 2.4.99.1) (ST6Gal I). One unit of sialyltransferase is defined as the quantity that will transfer 1 micromol of N-acetylneuraminic acid from cytidine monophosphate (CMP)-N-acetylneuraminic acid to asialofetuin per min at pH 6.5 and 37 degrees C. The method described here requires as little as 10 microl total assay volume, thus reducing the consumption of reagents. In addition, the sample is completely recoverable from the sensor chip surface, which allows for downstream analysis of the reaction product if desired. This method eliminates the need for labeled donor and acceptor molecules and does not require the separation of the substrates from the product before analysis. Although some kinetic properties of the enzyme can be estimated using this method, further development and validation is required. The method is most useful in determining qualitative estimates of ST6Gal I activity in tissue extracts and in characterizing the production of enzymes in cultured cell systems. The use of a microtiter plate assay format enables the rapid screening of multiple fractions for sialyltransferase activity.
Effects of transfusion with red cells filtered to remove leucocytes: randomised controlled trial in patients undergoing major surgery

Abstract Objective To compare postoperative complications in patients undergoing major surgery who received non-filtered or filtered red blood cell transfusions. Design Prospective, randomised, double blinded trial. Setting 19 hospitals throughout the Netherlands (three university; 10 clinical; six general). Participants 1051 evaluable patients: 79 patients with ruptured aneurysm, 412 patients undergoing elective surgery for aneurysm, and 560 undergoing gastrointestinal surgery. Interventions The non-filtered products had the buffy coat removed and were plasma reduced. The filtered products had the buffy coat removed, were plasma reduced, and filtered before storage to remove leucocytes. Main outcome measures Mortality and duration of stay in intensive care. Secondary end points were occurrence of multi-organ failure, infections, and length of hospital stay. Results No significant differences were found in mortality (odds ratio for filtered v non-filtered 0.80, 95% confidence interval 0.53 to 1.21) and in mean stay in intensive care (- 0.4 day, - 1.6 to 0.6 day). In the filtered group the mean length of hospital stay was 2.4 days shorter (- 4.8 to 0.0 day; P = 0.050) and the incidence of multi-organ failure was 30% lower (odds ratio 0.70, 0.49 to 1.00; P = 0.050). There were no differences in rates of infection (0.98, 0.73 to 1.32). Conclusion The use of filtered transfusions in some types of major surgery may reduce the length of hospital stay and the incidence of postoperative multi-organ failure.
Changes to the septo-fornical area might play a role in the pathogenesis of anxiety in multiple sclerosis

Background: Reports on the relationships between white matter lesion load (WMLL) and fatigue and anxiety in multiple sclerosis (MS) are inconsistent. Objective: To investigate the association of total and tract-specific WMLL with fatigue and anxiety. Methods: Total and regional T2 WMLL was assessed for 19 tracts in 48 MS patients (30 females). ICBM-DTI-81 Atlas-based parcellation was combined with WMLL segmentation of T2-weighted magnetic resonance imaging (MRI). Fatigue, anxiety, and depression were assessed using Fatigue Impact Scale, State Trait Anxiety Inventory, and Beck Depression Inventory, respectively. Results: Fatigue, anxiety, and depression showed significant inter-correlation. We found no association between fatigue and total or regional WMLLs, whereas anxiety was associated with total and regional WMLLs in nine tracts. After adjusting for total WMLL, age, and depression, only the column and body of the fornix (CBF) remained significantly associated with anxiety. Post hoc analyses showed no CBF lesions on T1-weighted MRI and suggested, but could not confirm, that the septum pellucidum might play a role in the pathogenesis of anxiety. Conclusion: Our results suggest that anxiety in MS patients may have a neuropathological substrate in the septo-fornical area, which requires further validation using larger sample size and ultra-high-field MRI in targeted prospective studies.
Social cognitive development : frontiers and possible futures

List of contributors Editorial preface 1. The 'intuitive scientist' formulation and its developmental implications Lee Ross 2. The development of thoughts about animate and inanimate objects: implications for research on social cognition Rochel Gelman and Elizabeth Spelke 3. Perspectives on the difference between understanding people and understanding things: the role of affect Martin L. Hoffman 4. 'Concrete thinking' and the development of social cognition Stephen M. Kosslyn and Jerome Kagan 5. Social cognition in a script framework Katherine Nelson 6. Role taking and social judgment: alternative developmental perspectives and processes E. Tory Higgins 7. Exploring children's social cognition on two fronts William Damon 8. Relations between social cognition, nonsocial cognition, and social behavior: the case of friendship Thomas J. Berndt 9. Self-referent thought: a developmental analysis of self-efficacy Albert Bandura 10. Metacognition and the rules of delay Water Mischel 11. Monitoring social cognitive enterprises: something else that may develop in the area of social cognition John H. Flavell 12. The moral intuitions of the child Richard A. Schweder, Elliot Turiel, and Nancy C. Much 13. Concluding remarks John H. Flavell and Lee Ross Index.