Miracle-dz/UniFAR-FTUs huggingface dataset:
Some Mathematical Refinements Concerning Error Minimization in the Genetic Code

The genetic code is known to have a high level of error robustness and has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimization problem as a Quadratic Assignment Problem and use this to formally verify that the code found by the heuristic algorithm is the global optimum. We also argue that it is strongly misleading to compare the genetic code only with codes sampled from the fixed block model, because the real code space is orders of magnitude larger. We thus enlarge the space from which random codes can be sampled from approximately 2.433 × 1018 codes to approximately 5.908 × 1045 codes. We do this by leaving the fixed block model, and using the wobble rules to formulate the characteristics acceptable for a genetic code. By relaxing more constraints, three larger spaces are also constructed. Using a modified error function, the genetic code is found to be more error robust compared to a background of randomly generated codes with increasing space size. We point out that these results do not necessarily imply that the code was optimized during evolution for error minimization, but that other mechanisms could be the reason for this error robustness.
Identification of Genes and Genomic Islands Correlated with High Pathogenicity in Streptococcus suis Using Whole Genome Tilling Microarrays

Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST), ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP) ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs). Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP.
The autism epidemic: fact or artifact?

OBJECTIVE We provide an illustration of how changes in methodological factors may produce variations in the frequency of autistic disorder (AD) over time and project how much of the observed increase in the frequency of AD may be explained by methodological factors. METHOD Using a prediction analysis, we calculate how broadening diagnostic criteria, younger age at diagnosis, and improved efficiency of case ascertainment could produce temporal trends in the incidence and prevalence of AD, measured by calendar year and by year of birth, in a hypothetical population of children 0 to 18 across the years 1950 to 2020. RESULTS Time trend studies report an increase as large as 11.0-fold over a 13-year period for AD. Conservative changes in the three methodological factors produced increases in the frequency of AD ranging from 2.1- to 28.8-fold. Measures of frequency by year of birth show the largest magnitude of increase; predicted prevalence by calendar year and to age 4 by year of birth are influenced by changes in the distribution of age at diagnosis, but 1-year incidence and prevalence to age 12 are not. DISCUSSION Methodological factors may explain the observed increases in AD over time. To increase confidence in reports of time trends, we recommend particular frequency measures and study circumstances.
A Randomized Cross-over Air Filtration Intervention Trial for Reducing Cardiovascular Health Risks in Residents of Public Housing near a Highway

Exposure to traffic-generated ultrafine particles (UFP; particles <100 nm) is likely a risk factor for cardiovascular disease. We conducted a trial of high-efficiency particulate arrestance (HEPA) filtration in public housing near a highway. Twenty residents in 19 apartments living <200 m from the highway participated in a randomized, double-blind crossover trial. A HEPA filter unit and a particle counter (measuring particle number concentration (PNC), a proxy for UFP) were installed in living rooms. Participants were exposed to filtered air for 21 days and unfiltered air for 21 days. Blood samples were collected and blood pressure measured at days 0, 21 and 42 after a 12-hour fasting period. Plasma was analyzed for high sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), tumor necrosis factor alpha-receptor II (TNF-RII) and fibrinogen. PNC reductions ranging from 21% to 68% were recorded in 15 of the apartments. We observed no significant differences in blood pressure or three of the four biomarkers (hsCRP, fibrinogen, and TNF-RII) measured in participants after 21-day exposure to HEPA-filtered air compared to measurements after 21-day exposure to sham-filtered air. In contrast, IL-6 concentrations were significantly higher following HEPA filtration (0.668 pg/mL; CI = 0.465–0.959) compared to sham filtration. Likewise, PNC adjusted for time activity were associated with increasing IL-6 in 14- and 21-day moving averages, and PNC was associated with decreasing blood pressure in Lags 0, 1 and 2, and in a 3-day moving average. These negative associations were unexpected and could be due to a combination of factors including exposure misclassification, unsuccessful randomization (i.e., IL-6 and use of anti-inflammatory medicines), or uncontrolled confounding. Studies with greater reduction in UFP levels and larger sample sizes are needed. There also needs to be more complete assessment of resident time activity and of outdoor vs. indoor source contributions to UFP exposure. HEPA filtration remains a promising, but not fully realized intervention.
Linking Increasing Drought Stress to Scots Pine Mortality and Bark Beetle Infestations

In the dry Swiss Rhone Valley, Scots pine forests have experienced increased mortality in recent years. It has commonly been assumed that drought events and bark beetles fostered the decline, however, whether bark beetle outbreaks increased in recent years and whether they can be linked to drought stress or increasing temperature has never been studied. In our study, we correlated time series of drought indices from long-term climate stations, 11-year mortality trends from a long-term research plot, and mortality probabilities modeled from tree rings (as an indicator of tree vitality) with documented occurrences of various bark beetle species and a buprestid beetle, using regional Forest Service reports from 1902 to 2003 and advisory cases of the Swiss Forest Protection Service (SFPS) from 1984 to 2005. We compared the historical findings with measured beetle emergence from a 4-year tree felling and breeding chamber experiment. The documented beetle-related pine mortality cases increased dramatically in the 1990s, both in the forest reports and the advisory cases. The incidents of beetle-related pine mortality correlated positively with spring and summer temperature, and with the tree-ring-based mortality index, but not with the drought index. The number of advisory cases, on the other hand, correlated slightly with summer drought index and temperature, but very highly with tree–ring—based mortality index. The tree-ring-based mortality index and observed tree mortality increased in years following drought. This was confirmed by the beetle emergences from felled trees. Following dry summers, more than twice as many trees were colonized by beetles than following wet summers. We conclude that increased temperatures in the Swiss Rhone Valley have likely weakened Scots pines and favored phloeophagous beetle population growth. Beetles contributed to the increased pine mortality following summer drought. Among the factors not addressed in this study, changed forest use may have also contributed to increased beetle populations and Scots pine mortality, whereas air pollution seems to be of lesser importance.
Variable Variation: Annual and Seasonal Changes in Offspring Sex Ratio in a Bat

Many organisms produce offspring with sex-ratios that deviate from equal numbers of males and females, and numerous adaptive explanations have been proposed. In some species, offspring sex-ratio varies across the reproductive season, again with several explanations as to why this might be adaptive. However, patterns for birds and mammals are inconsistent, and multiple factors are likely involved. Long-term studies on a variety of species may help untangle the complexity. I analyzed a long-term data set on the variation in offspring sex-ratio of the big brown bat, Eptesicus fuscus, a temperate-zone, insectivorous species. Sex ratio varied seasonally, but only in some years. Births early in the season were significantly female biased in years in which parturition occurred relatively early, but not in years with late parturition. Survival of female pups increased with earlier median birth date for the colony, and early-born females were more likely to survive and reproduce as one-year olds, compared to later-born pups. I argue that, due to the unusual timing of reproductive activities in male and female bats that hibernate, producing female offspring early in the year increases their probability of reproducing as one year olds, but this is not the case for male offspring. Thus, mothers that can give birth early in the year, benefit most by producing a female pup. The relative benefit of producing female or male offspring varies depending on the length of the growing season and thus the time available for female pups to reach sexual maturity. This suggests that not only does sex-ratio vary seasonally and among years, depending on the condition of the mother and the environment, but also likely varies geographically due to differences in season length.
A nonlinear manifold learning framework for real-time motion estimation using low-cost sensors

We propose a real-time motion synthesis framework to control the animation of 3D avatar in real-time. Instead of relying on motion capture device as the control signal, we use low-cost and ubiquitously available 3D accelerometer sensors. The framework is developed under a data-driven fashion, which includes two steps: model learning from existing high quality motion database, and motion synthesis from the control signal. In the model learning step, we apply a non-linear manifold learning method to establish a high dimensional motion model which learned from a large motion capture database. Then, by taking 3D accelerometer sensor signal as input, we are able to synthesize high-quality motion from the motion model we learned from the previous step. The system is performing in real-time, which make it available to a wide range of interactive applications, such as character control in 3D virtual environments and occupational training.
MicroRNA-7a/b Protects against Cardiac Myocyte Injury in Ischemia/Reperfusion by Targeting Poly(ADP-Ribose) Polymerase

Objectives MicroRNA-7 (miR-7) is highly connected to cancerous cell proliferation and metastasis. It is also involved in myocardial ischemia-reperfusion (I/R) injury and is upregulated in cardiomyocyte under simulated I/R (SI/R). We aimed to investigate the role of miR-7 during myocardial I/R injury in vitro and in vivo and a possible gene target. Methods and Results Real-time PCR revealed that miR-7a/b expression was upregulated in H9c2 cells after SI/R. Flow cytometry showed SI/R-induced cell apoptosis was decreased with miR-7a/b mimic transfection but increased with miR-7a/b inhibitor in H9c2 cells. In a rat cardiac I/R injury model, infarct size determination and TUNEL assay revealed that miR-7a/b mimic decreased but miR-7a/b inhibitor increased cardiac infarct size and cardiomyocyte apoptosis as compared with controls. We previously identified an important gene connected with cell apoptosis -- poly(ADP-ribose) polymerase (PARP) -- as a candidate target for miR-7a/b and verified the target by luciferase reporter activity assay and western blot analysis. Conclusions miR-7a/b is sensitive to I/R injury and protects myocardial cells against I/R-induced apoptosis by negatively regulating PARP expression in vivo and in vitro. miR-7a/b may provide a new therapeutic approach for treatment of myocardial I/R injury. Poly(ADP-ribose) polymerase.
Interviewers’ Characteristics and Post-Hire Attitudes and Performance

Many studies have demonstrated the impact of interviewers’ characteristics on applicants’ reactions in terms of their impressions of the organization and their intentions to accept the job offer. However, previous research has generally neglected the effect of interviewers’ characteristics on applicants after they join the firm. The present study, which involved a sample of 200 employees from different industries, showed that interviewers’ characteristics significantly affect applicants’ job satisfaction, motivation, and performance after they were hired in the firm. However, the results did not show support for the proposed effect of interviewers’ characteristics on organizational commitment. Discussions and conclusions are presented.
The Role of Thymus-Expressed Chemokine and Its Receptor CCR9 on Lymphocytes in the Regional Specialization of the Mucosal Immune System1

Chemokines play an important role in the migration of leukocytes at sites of inflammation, and some constitutively expressed chemokines may direct lymphocyte trafficking within lymphoid organs and peripheral tissues. Thymus-expressed chemokine (TECK or Ckβ-15/CCL25), which signals through the chemokine receptor CCR9, is constitutively expressed in the thymus and small intestine but not colon, and chemoattracts a small fraction of PBLs that coexpress the integrin α4β7. Here we show that TECK is expressed in the human small bowel but not colon by endothelial cells and a subset of cells in intestinal crypts and lamina propria. CCR9 is expressed in the majority of freshly isolated small bowel lamina propria mononuclear cells (LPMC) and at significantly higher levels compared with colonic LPMC or PBL. TECK was selectively chemotactic for small bowel but not colonic LPMC in vitro. The TECK-induced chemotaxis was sensitive to pertussis toxin and partially inhibited by Abs to CCR9. TECK attracts predominantly the T cell fraction of small bowel LPMC, whereas sorted CD3+CCR9+ and CD3+CCR9− lymphocytes produce similar Th1 or Th2 cytokines at the single cell level. Collectively, our data suggest that the selective expression of TECK in the small bowel underlie the homing of CCR9+ intestinal memory T cells to the small bowel rather than to the colon. This regional specialization implies a segregation of small intestinal from colonic immune responses.
The Role of Model-Based Segmentation in the Recovery of Volumetric Parts From Range Data

We present a method for segmenting and estimating the shape of 3D objects from range data. The technique uses model views, or aspects, to constrain the fitting of deformable models to range data. Based on an initial region segmentation of a range image, regions are grouped into aspects corresponding to the volumetric parts that make up an object. The qualitative segmentation of the range image into a set of volumetric parts not only captures the coarse shape of the parts, but qualitatively encodes the orientation of each part through its aspect. Knowledge of a part's coarse shape, its orientation, as well as the mapping between the faces in its aspect and the surfaces on the part provides strong constraints on the fitting of a deformable model (supporting both global and local deformations) to the data. Unlike previous work in physics-based deformable model recovery from range data, the technique does not require presegmented data. Furthermore, occlusion is handled at segmentation time and does not complicate the fitting process, as only 3D points known to belong to a part participate in the fitting of a model to the part. We present the approach in detail and apply it to the recovery of objects from range data.
Surgical treatment of nonalcoholic fatty liver disease in severely obese patients

Obesity is a multi-organ system disease with underlying metabolic abnormalities and chronic systemic inflammation. Nonalcoholic fatty liver disease (NAFLD) is a hepatic manifestation of obesity metabolic dysfunction and its associated cardiovascular- and liver-related morbidities and mortality. Our current understanding of NAFLD pathogenesis, disease characteristics, the role of insulin resistance, chronic inflammation, gut–liver and gut–brain crosstalk and the effectiveness of pharmacotherapy is still evolving. Bariatric surgery significantly improves metabolic and NAFLD histology in severely obese patients, although its positive effects on fibrosis are not universal. Bariatric surgery benefits NAFLD through its metabolic effect on insulin resistance, inflammation, and insulinotropic and anorexinogenic gastrointestinal hormones. Further studies are needed to understand the natural course of NAFLD in severely obese patients and the role of weight loss surgery as a primary treatment for NAFLD.
Intergenerational influences on early alcohol use: Independence from the problem behavior pathway

Abstract Conduct problems are a general risk factor for adolescent alcohol use. However, their role in relation to alcohol-specific risk pathways of intergenerational transmission of alcohol use is not well understood. Further, the roles of alcohol-specific contextual influences on children's early alcohol use have been little examined. In a 20-year prospective, multimethod study of 83 fathers and their 125 children, we considered the predictors of child alcohol use by age 13 years. The predictors included fathers' adolescent antisocial behavior and alcohol use, both parents' adult alcohol use, norms about and encouragement of child use, parental monitoring, child-reported exposure to intoxicated adults, and parent-reported child externalizing behaviors. Path models supported an association between fathers' adolescent alcohol use and children's use (β = 0.17) that was not better explained by concurrent indicators of fathers' and children's general problem behavior. Fathers' and mothers' adult alcohol use uniquely predicted child use, and exposure to intoxicated adults partially mediated the latter path. Other family risk mechanisms were not supported. However, parental alcohol use and child alcohol use were linked in expected ways with family contextual conditions known to set the stage for alcohol use problems later in adolescence.
Influence of feed enriched with natural antioxidants on the oxidative stability of broiler meat

The effect of feed supplementation with natural α-tocopherol, rosemary, green tea, grape seed and tomato extracts on the oxidative stability of broiler meat was investigated by measuring lipid oxidation, protein oxidation and α-tocopherol content of breast muscle. Supplementation with α-tocopheryl acetate at a dietary concentration of 200 ppm was used as a control. The broilers were fed a diet containing 4% linseed oil for 6 weeks. The antioxidant extracts were supplemented in single and in combinations at total concentrations of 100 and 200 ppm. For lipid oxidation, the 200 ppm αtocopheryl acetate treatment yielded the lowest TBARS values. Dose effects were observed for αtocopherol, grape seed and tomato, while no dose effect was observed for rosemary. In contrast, green tea showed a pro-oxidative effect at 200 ppm. Combinations of α-tocopherol, rosemary and green tea did not reveal synergistic effects between the different extracts and strengthened the hypothesis of the pro-oxidative effect of green tea at higher doses. No differences between the different antioxidant treatments were detected for protein oxidation. The muscle α-tocopherol content linearly responded to the feed α-tocopherol content. No differences in α-tocopherol deposition was observed between the natural or the synthetic form.
Discrete parameter-nonlinear constrained optimisation of a gear train using genetic algorithms

This paper investigates the optimal design of a four-stage gear train using genetic algorithms. Five different genetic encoding schemes, which incorporate various heuristic search techniques, are proposed to deal with the most critical constraints of the problem. The fitness criterion used by all genetic algorithms includes a merit function for minimising the size of the gearbox. The results show improvement in the design merit over previous approaches without reliance on the designer's interaction to avoid geometric constraint violations and facilitate the convergence.
Direct Validation of TRMM/PR Near Surface Rain over the Northeastern Indian Subcontinent Using a Tipping Bucket Raingauge Network

The near surface rain (NSR) dataset of the Tropical Rainfall Measurement Mission (TRMM) Precipitation Radar (PR) 2A25 V7 was validated using 36 tipping bucket raingauges installed over the northeastern Indian subcontinent, which correspond with the rain center of the Asian summer monsoon. This raingauge network covers the Brahmaputra flood plains and mountainous areas, including the Meghalaya Plateau, which is one of the wettest places in the world. We analyzed data from 2004 to 2013, and obtained 28,207 TRMM/PR-raingauge matchups with 2,170 TRMM/PR rainy field of views. Using them, we detected a reasonable time lag of around 300 seconds between the estimates from the TRMM/PR NSR and raingauges. Significant and large underestimations of TRMM/PR NSR were detected during the monsoon season (June–September) over the large areas of Meghalaya, Sylhet, and Barak. The bias ratios were −51.3% and −35.2% for the Meghalaya and Sylhet-Barak areas, respectively. In the Meghalaya subregion, major contribution to underestimation came from moderate TRMM/PR NSR from stratiform systems, and missed detection error was secondary contributor. In Sylhet-Barak subregion, moderate TRMM/PR NSR from convective systems largely contributed. Underestimation was not detected in premon - soon season (March–May). over Japan. But they did not proceed to the comparison among different season and topographic features. Prat and Barros (2010) investigated the orographic effect on the TRMM/PR NSR accuracy using raingauges, identifying large underestimation in TRMM/PR NSR over the complex terrain in the Southern Appalachian mountains. They further noted that the underestimation reached −59% for the tropical storm case.