Miracle-dz/UniFAR-FTUs huggingface dataset:
University of Groningen Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci

The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment interaction, which is of great importance in many quantitative traits, can only be approached by separately analyzing the data collected in multiple environments. Here, we demonstrate for the first time a novel analytic approach (MQM mapping) that accommodates both the mapping of multiple QTLs and genotype-by-environment interaction. MQM mapping is compared to interval mapping in the mapping of QTLs for flowering time in Arabidopsis thaliana under various photoperiod and vernalization conditions.
Elecciones 2012: en busca de equidad y legalidad

Dentro de la rica producción de libros que ha dejado la reforma electoral 2007-2008 aparece, en forma destacada, la compilación que hace John Ackerman de 26 ensayos analíticos resultado del seminario “Elecciones 2012: en busca de equidad y legalidad”, que fue organizado por el Instituto de Investigaciones Jurídicas de la UNAM y el Programa de las Naciones Unidas para el Desarrollo (PNUD) en octubre de 2010. Se trata de un texto en el que participan magistrados y consejeros electorales, académicos y legisladores, y en el que el lector encontrará análisis que van desde las visiones de conjunto de la reforma electoral hasta aspectos muy particulares de ajustes y/o correcciones en la materia.
Impact of Recipient Body Mass Index on Short-Term and Long-Term Survival of Pancreatic Grafts

Background The impact of recipient body mass index on graft and patient survival after pancreas transplantation is not well known. Methods We have analyzed data from all pancreas transplant recipients reported in the Scientific Registry of Transplant Recipients between 1987 and 2011. Recipients were categorized into BMI classes, as defined by the World Health Organization. Short-term (90 days) and long-term (90 days to 5 years) patient and graft survivals were analyzed according to recipient BMI class using Kaplan-Meier estimates. Hazard ratios were estimated using Cox proportional hazard models. Results A total of 21,075 adult recipients were included in the analysis. Mean follow-up was 5±1.1 years. Subjects were overweight or obese in 39%. Increasing recipient BMI was an independent predictor of pancreatic graft loss and patient death in the short term (P<0.001), especially for obese class II patient survival (hazard ratio, 2.07; P=0.009). In the long term, obesity, but not overweight, was associated with higher risk of graft failure (P=0.01). Underweight was associated with a higher risk of long-term death (P<0.001). Conclusion These results question the safety of pancreas transplantation in obese patients and suggest that they may be directed to alternate therapies, such as behavioral modifications or bariatric surgery, before pancreas transplantation is considered.
Cohesive Subgraph Mining on Attributed Graph

Finding cohesive subgraphs is a fundamental graph problem with a wide spectrum of applications. In this paper, we investigate this problem in the context of attributed graph, where each vertex is associated with content (e.g., geo-locations, tags and keywords). To properly capture the cohesiveness of the vertices in a subgraph from both graph structure and vertices attribute perspectives, we advocate a novel cohesive subgraph model, namely (k,r)-core. In particular, we adopt the popular concept of k-core as the structural constraint such that each vertex in a (k,r)-core connects to at least k other vertices. Meanwhile, there is a user defined similarity threshold (i.e., similarity constraint) to ensure that the contents of the vertices in the same (k,r)-core are similar to each other. We aim to devise efficient algorithms to enumerate all maximal (k,r)-cores and find the maximum (k,r)core, where both problems are shown to be NP-hard. Effective end efficient pruning techniques are proposed to significantly reduce the search space of two algorithms. Novel double k-core based upper bound computation method is also devised to enhance the performance of the maximum (k,r)-core computation algorithm. According to the different nature of two mining algorithms, we devise effective search orders. Our comprehensive experiments on real-life data demonstrate that the maximal/maximum (k,r)cores enable us to find interesting cohesive subgraphs, and the performance of two mining algorithms is significantly improved by our effective pruning techniques and smart search orders.
Mutual functional antagonism of the simian virus 40 T antigen and the hepatitis B virus trans activator

The hepatitis B virus X protein (pX) trans activates transcription of a wide variety of viral and cellular genes, apparently by interacting with multiple cellular transcription factors. It has been shown previously that the simian virus 40 early-region gene products (large-T and small-t antigens) prevent trans activation by pX. We show here that this phenomenon can be ascribed solely to the large-T antigen and that T antigen binds to pX in vitro. Mapping studies reveal that the region of large-T antigen around residues 125 and 126 is critical for this binding and also for the ability of T antigen to prevent trans activation by pX. Furthermore, pX in turn interferes with two of the known functions of T antigen, transcriptional trans activation and simian virus 40 DNA replication. We propose that pX and T antigen inactivate each other by forming a nonfunctional complex in vivo.
Surviving emergency social work: experience of an Australian Accident & Emergency Department.

Thoughts go through my head: I don’t need this today; that’s a new name. I don’t know him; oh well-nothing much I can do. Maybe he’ll leave once he’s slept it off. The day goes on. The wards are busy. The Friday clear-out is on. Emergency want me again and again. And Stat’s are due today. Page #2 is at 9.30: an elderly lady has turned up in casualty not knowing why she is here or who sent her . a bit of investigation reveals she is dementing and has come to the hospital to go to the attached Day Centre — Friday is her day, but she had forgotten. Page #3 is at midday: a young man I had seen a week ago has arrived wanting to find out what his ex-girlfriend has done with his child while she is in the Psych. Unit. On my second visit to the Emergency Department I check on John D. I read his notes,
Theoretical and practical comparisons of the reassignment method and the derivative method for the estimation of the frequency slope

In the context of non-stationary sinusoidal analysis, the theoretical comparison of the reassignment method (RM) and the derivative method (DM) for the estimation of the frequency slope is investigated. It is shown that for the estimation of the frequency slope the DM differs from the RM in that it does not consider the group delay. Theoretical equivalence is shown to be possible with a refinement of the DM. This refinement is evaluated on synthetic signals and shown to improve the estimation of the frequency slope. The differences between the two methods in terms of window and signal constraints are discussed to show when each method is more appropriate to use.
Comparison of design concepts for AC low voltage distribution networks

The progression of embedded generation in distribution networks combined with an expanding use of electricity for mobility, heating and air conditioning leads to an increased loading of the distribution networks. These incoming challenges and their consequences make us reflect whether it is reasonable to retain the present design concepts and paradigms. The paper analyzes the required capabilities of the future low voltage distribution networks, expressing them in terms of demand and coincidence of the demand. Based on these requirements, various design concept scenarios are developed and tested on an exemplary network topology. Rather than adjusting the cross section of the cables or adding substations to the network (to reduce the distance between substations and delivery points), the nominal voltage and the voltage tolerance range are varied. This basic investigation forms the evolution paths for low voltage distribution systems and provides a platform for further discussion. A change in design paradigms is laborious, but a well prepared transition of the systems' design concepts has the potential to be a more economical solution than the unquestioned use of aged design concepts.
Long-term safety and tolerability of lurasidone in schizophrenia: a 12-month, double-blind, active-controlled study

The aim of this study is to evaluate the long-term safety and tolerability of lurasidone in the treatment of schizophrenia. Clinically stable adult outpatients with schizophrenia were randomized in a 2 : 1 ratio to 12 months of double-blind treatment with once-daily, flexibly-dosed lurasidone (40–120 mg) or risperidone (2–6 mg). Outcome measures included adverse events (AEs), vital signs, ECG, and laboratory tests. Secondary assessments included measures of psychopathology. A total of 427 patients were randomized to treatment with lurasidone and 202 with risperidone. The three most frequent AEs in the lurasidone group (vs. risperidone) were nausea (16.7 vs. 10.9%), insomnia (15.8 vs. 13.4%), and sedation (14.6 vs. 13.9%); the three most frequent AEs in the risperidone group (vs. lurasidone) were increased weight (19.8 vs. 9.3%), somnolence (17.8 vs. 13.6%), and headache (14.9 vs. 10.0%). A higher proportion of patients receiving risperidone had at least a 7% endpoint increase in weight (14 vs. 7%). The median endpoint change in prolactin was significantly higher for risperidone (P<0.001). A comparable improvement in efficacy measures was observed with both agents and the rates of relapse were similar. All-cause discontinuation rates were higher for lurasidone versus risperidone. Long-term treatment with lurasidone was generally well tolerated in this study, with minimal effects on weight and metabolic outcomes.
Stimulated osteoclastic and suppressed osteoblastic activity in metabolic but not respiratory acidosis.

When bone is cultured in acidic medium produced by a reduced bicarbonate concentration ([HCO(3-)]), a model of metabolic acidosis, there is greater net calcium efflux than when the same decrement in pH is produced by an increased partial pressure of carbon dioxide (PCO2), a model of respiratory acidosis. To determine the effects of metabolic and respiratory acidosis on bone cell function we cultured neonatal mouse calvariae for 48 h under control conditions (pH approximately 7.40, PCO2 approximately 41 mmHg, [HCO(3-)] approximately 25 meq/l) or under isohydric acidic conditions simulating metabolic (pH approximately 7.09, [HCO(3-)] approximately 12) or respiratory (pH approximately 7.10, PCO2 approximately 86) acidosis and measured osteoblastic collagen synthesis and alkaline phosphatase activity and osteoclastic beta-glucuronidase activity. Collagen synthesis was inhibited by metabolic (23.2 +/- 1.3 vs. 30.3 +/- 1.0% in control) but was not altered by respiratory (32.3 +/- 0.6) acidosis. Alkaline phosphatase activity was inhibited by metabolic (402 +/- 16 vs. 471 +/- 15 nmol P.min-1.mg protein-1 in control) but not altered by respiratory (437 +/- 25) acidosis. beta-Glucuronidase activity was stimulated by metabolic (1.02 +/- 0.06 vs. 0.78 +/- 0.05 micrograms phenolphthalein released.bone-1.h-1 in control) but not altered by respiratory (0.73 +/- 0.06) acidosis. Net calcium efflux in control was increased by metabolic (783 +/- 57 vs. 20 +/- 57 nmol.bone-1.48 h-1 in control) and by respiratory (213 +/- 45) acidosis; however, calcium efflux with metabolic was greater than with respiratory acidosis. (ABSTRACT TRUNCATED AT 250 WORDS)
Involvement of CD8+ T-cells in exacerbation of corneal scarring in mice

Purpose. To determine the specific immune responses involved in the exacerbation of corneal scarring induced by HSV-1 in gK vaccinated mice. Materials and methods. BALB/c mice were vaccinated with HSV-1 glycoprotein K (gK) and ocularly challenged with HSV-1. Infiltration into the cornea of T cells and macrophages was monitored by immunocytochemistry, and the effect of depletion of CD4+ T-cells, CD8+ T-cells, or macrophages on corneal scarring was determined. Results. Following ocular challenge, CD4+ and CD8+ T-cells and macrophages were more abundant in the corneas of gK-vaccinated mice than in the corneas of mock vaccinated mice. Depletion of CD8+ T-cells, but not of CD4+ T-cells or macrophages, reduced the severity of corneal scarring in gK-vaccinated mice. Conclusions. We have shown that gK vaccination causes an overall increase in T cells and macrophages in the cornea after ocular HSV-1 challenge. The immunopathology induced by gK vaccination appears to be related to CD8+ T-cell activity, as depletion of these cells, but not other immune cells, reduced corneal scarring.
Effects of nonthermal preservation technologies on antioxidant activity of fruits and vegetables: A review

Consumer demand for safe and nutritious fruits and vegetables has given rise to the development of a number of nonthermal food preservation techniques. Recent studies have highlighted that antioxidant activity of fruits and vegetables plays an important role in human health. In this paper, the influences of nonthermal preservation technologies, including pulsed electric field, radiation processing, dense phase carbon dioxide, ozone processing, and edible coatings, on the antioxidant capacity and related compounds in fruits and vegetables are reviewed. The proposed mechanisms and future trends are also discussed to accelerate the further commercialization and exploration of these novel technologies, which will, in turn, help to promote human health.
Vascular-bed--specific hemostasis and hypercoagulable states.

Hemostasis is a physiologic mechanism that maintains blood in a fluid state within the circulation. The coagulation of blood is mediated by cellular components and soluble plasma proteins. In response to vascular injury, circulating platelets adhere, aggregate, and provide cell-surface phospholipid for the assembly of blood-clotting enzyme complexes. The extrinsic pathway of blood coagulation is initiated when blood is exposed to non-vascular-cell–bound tissue factor in the subendothelial space (Figure 1). Tissue factor binds to activated factor VII, and the resulting enzyme complex activates factors IX and X of the intrinsic and common coagulation pathways, respectively. Factor IX activated by the .
Community-associated methicillin-resistant Staphylococcus aureus in a pediatric emergency department in Newfoundland and Labrador.

BACKGROUND First-generation cephalosporins and antistaphylococcal penicillins are typically the first choice for treating skin and soft tissue infections (SSTI), but are not effective for infections caused by methicillin-resistant Staphylococcus aureus (MRSA). It is currently unclear what percentage of SSTIs is caused by community-associated MRSA in different regions in Canada. OBJECTIVES To determine the incidence of MRSA in children presenting to a pediatric emergency department with SSTI, and to determine which antibiotics were used to treat these infections. METHODS All visits to a pediatric emergency department were reviewed from April 15, 2010 to April 14, 2011. Diagnoses of cellulitis, abscess, impetigo, folliculitis and skin infection (not otherwise specified) were reviewed in detail to determine whether a culture was taken and which antibiotic was prescribed. RESULTS There were 367 cases of SSTI diagnosed over the study period. Forty-five (12.3%) patients had lesions that were swabbed for culture and sensitivity. S aureus was the most common organism found, with 14 (66%) methicillin-sensitive cases and seven (33%) methicillin-resistant cases. Of the seven cases of MRSA identified, only one patient had clear risk factors for hospital-acquired MRSA. First-generation cephalosporins were initially prescribed for 280 (76%) patients. CONCLUSIONS The overall incidence of MRSA in the population presenting to a pediatric emergency department in Newfoundland and Labrador appeared to be low, although only a small percentage of infections were cultured. At this time, there appears to be no need to change empirical antibiotic coverage, which remains a first-generation cephalosporin.
Re-implementing and Extending a Hybrid SAT-IP Approach to Maximum Satisfiability

Real-world optimization problems, such as those found in logistics and bioinformatics, are often NP-hard. Maximum satisfiability (MaxSAT) provides a framework within which many such problems can be efficiently represented. MaxHS is a recent exact algorithm for MaxSAT. It is a hybrid approach that uses a SAT solver to compute unsatisfiable cores and an integer programming (IP) solver to compute minimum-cost hitting sets for the found cores. This thesis analyzes and extends the MaxHS algorithm. To enable this, the algorithm is re-implemented from scratch using the C++ programming language. The resulting MaxSAT solver LMHS recently gained top positions at an international evaluation of MaxSAT solvers. This work looks into various aspects of the MaxHS algorithm and its applications. The impact of different IP solvers on the MaxHS algorithm and the behavior induced by different strategies of postponing IP solver calls is examined. New methods of enhancing the computation of unsatisfiable cores in MaxHS are examined. Fast core extraction through parallelization by partitioning soft clauses is explored. A modification of the final conflict analysis procedure of a SAT solver is used to generate additional cores without additional SAT solver invocations. The use of additional constraint propagation procedures in the SAT solver used by MaxHS is investigated. As a case study, acyclicity constraint propagation is implemented and its effectiveness for bounded treewidth Bayesian network structure learning using MaxSAT is evaluated. The extension of MaxHS to the labeled MaxSAT framework, which allows for more efficient use of preprocessing techniques and group MaxSAT encodings in MaxHS, is discussed. The re-implementation of the MaxHS algorithm, LMHS, also enables incrementality in efficiently adding constraints to a MaxSAT instance during the solving process. As a case study, this incrementality is used in solving subproblems with MaxSAT within GOBNILP, a tool for finding optimal Bayesian network structures.
Why the tuberculosis incidence rate is not falling in New Zealand.

AIMS To assess the role of migration from high-incidence countries, HIV/AIDS infection, and prevalence of multi-drug resistant organisms as contributors to tuberculosis (TB) incidence in New Zealand (NZ) relative to ongoing local transmission and reactivation of disease. METHODS TB notification data and laboratory data for the period 1995 to 2004 and population data from the 1996 and 2001 Census were used to calculate incidence rates of TB by age and ethnicity, country of birth (distinguishing high and low -incidence countries), and interval between migration and onset of disease. Published reports of multi-drug-resistant TB for the period 1995 to 2004 were reviewed. Anonymous HIV surveillance data held by AIDS Epidemiology Group were matched with coded and anonymised TB surveillance data to measure the extent of HIV/AIDS coinfection in notified TB cases. RESULTS Migration of people from high-TB incidence countries is the main source of TB in NZ. Of those who develop TB, a quarter does so within a year of migration, and a quarter of this group (mainly refugees) probably enter the country with pre-existing disease. Rates of local TB transmission and reactivation of old disease are declining steadily for NZ-born populations, except for NZ-born Maori and Pacific people under 40. HIV/AIDS and multi-drug-resistant organisms are not significant contributors to TB incidence in NZ and there is no indication that their role is increasing. CONCLUSION TB incidence is not decreasing in NZ mainly due to migration of TB infected people from high-incidence countries and subsequent development of active disease in some of them in NZ. This finding emphasises the importance of regional and global TB control initiatives. Refugees and migrants are not acting as an important source of TB for most NZ-born populations. Those caring for them should have a high level of clinical suspicion for TB.
A 2.4 GHz Low-Power Sixth-Order RF Bandpass $\Delta\Sigma$ Converter in CMOS

A sixth-order RF bandpass DeltaSigma ADC operating on the 2.4 GHz ISM band, which is suitable for RF digitization is presented. The bandpass loop filter is based on digitally programmable Gm-LC resonators that can be calibrated online to adjust the RF center frequency. By sampling below the input Nyquist frequency, the clock in the system was reduced to 3 GHz, allowing a large reduction of the power consumption. Implemented in a standard 90 nm CMOS process, the IC achieves 40 dB and 62 dB of SNDR and SFDR, respectively, on a 60 MHz bandwidth with 40 mW of power consumption leading to a FoM of 245 GHz/W (4.1 pJ/conversion step). This implementation paves a possible way towards direct RF digitization receiver architectures.
The Utility of the Ces-D as a Depression Screening Measure among Low-Income Women Attending Primary Care Clinics

Objective: Depressive disorders are among the most common medical disorders seen in primary care practice. The Center for Epidemiologic Studies-Depression (CES-D) scale is one of the measures commonly suggested for detecting depression in these clinics. However, to our knowledge, there have been no previous studies examining the validity of the CES-D among low-income women attending primary care clinics. Method: Low-income women attending public primary care clinics (n = 179, ages 20–77) completed the CES-D and the Diagnostic Interview Schedule for the DSM-IV (DIS-IV). Results: The results supported the validity of the CES-D. The standard cut-score of 16 and above yielded a sensitivity of . 95 and specificity of . 70 in predicting Major Depressive Disorder (MDD). However, over two-thirds of those who screened positive did not meet criteria for MDD (positive predictive value = .28). The standard cut-score appears valid, but inefficient for depression screening in this population. An elevated cut-score of 34 yielded a higher specificity (.95) and over 50 percent of the patients who screened positive had a MDD (positive predictive value = .53), but at great cost to sensitivity (.45). Conclusion: Results indicated that the CES-D appears to be as valid for low-income, minority women as for any other demographic group examined in the literature. Despite similar validity, the CES-D appears to be inadequate for routine screening in this population. The positive predictive value remains very low no matter which cut-scores are used. The costs of the false positive rates could be prohibitive, especially in similar public primary care settings.