Miracle-dz/UniFAR-FTUs huggingface dataset:
Lifetime body mass index and later atherosclerosis risk in young adults: examining causal links using Mendelian randomization in the Cardiovascular Risk in Young Finns study

Aims Mendelian randomization uses genetic variants related to environmentally modifiable risk factors in an attempt to improve causal inference from observational data. We examined the effect of lifetime body mass index (BMI) on adult carotid intima-media thickness (CIMT) and various atherosclerotic risk factors by using both Mendelian randomization and conventional analyses. Methods and results A total of 2230 individuals (1218 women), aged 3–18 at study induction, took part in clinical examinations in 1980, 1983, 1986, and, most recently, 2001 when they were aged 24–39. In these analyses we utilized the known relation between FTO polymorphism rs9939609 and BMI. The dose–response association between the number of A alleles in FTO and higher mean BMI from childhood to adulthood was confirmed, but no associations with potential confounding factors were observed. In standard regression models, lifetime BMI was associated with adult CIMT, lifetime systolic blood pressure, adult fasting glucose, and adult HOMA-index. When variation in FTO was used as an instrument for unconfounded BMI levels, similar or larger effects of lifetime BMI on all these phenotypes were found, although with wider confidence intervals. Conclusion Mutually supportive results from Mendelian randomization and standard regression models strengthen the evidence of the effect of lifetime BMI on atherosclerosis risk in young adults.
Declines in Drp1 and Parkin Expression Underlie DNA Damage-Induced Changes in Mitochondrial Length and Neuronal Death

Maintaining proper mitochondrial length is essential for normal mitochondrial function in neurons. Mitochondrial fragmentation has been associated with neuronal cell death caused by a variety of experimental toxic stressors. Despite the fact that oxidative stress is a hallmark of neurodegenerative conditions and aging and the resulting activation of p53 is believed to contribute to the neuropathology, little is still known regarding changes in mitochondrial morphology in p53-dependent neuronal death. Therefore, we specifically addressed the relationship between genotoxic stress, p53 activation, and the regulation of mitochondrial morphology in neurons. In cultured postnatal mouse cortical neurons, treatment with the DNA-damaging agent camptothecin (CPT) resulted in elongated mitochondria, in contrast to fragmented mitochondria observed upon staurosporine and glutamate treatment. In fibroblasts, however, CPT resulted in fragmented mitochondria. CPT treatment in neurons suppressed expression of the mitochondrial fission protein Drp1 and the E3 ubiquitin ligase parkin. The presence of elongated mitochondria and the declines in Drp1 and parkin expression occurred before the commitment point for apoptosis. The CPT-induced changes in Drp1 and parkin were not observed in p53-deficient neurons, while p53 overexpression alone was sufficient to reduce the expression of the two proteins. Elevating Drp1 or parkin expression before CPT treatment enhanced neuronal viability and restored a normal pattern of mitochondrial morphology. The present findings demonstrate that genotoxic stress in neurons results in elongated mitochondria in contrast to fission induced by other forms of stress, and p53-dependent declines in Drp1 and parkin levels contribute to altered mitochondrial morphology and cell death.
The Effect of Essential Fatty Acids for the Somatic Growth in Nauplii of Calanus finmarchicus

The growth of Calanus finmarchicus nauplii was studied through three spawning seasons (2007, 2009 and 2011) using flow-through tubes. Natural seston was collected every second day and added as food source using a peristaltic pump. A mixture of cultured microalgae supplied in surplus concentration was used as a control treatment. No significant correlation between growth and food concentration measured as Chlorophyll a (Chla) or particulate organic carbon (POC) was detected, but the growth rate was significantly related to the content of EPA (20:5n-3) and DHA (22:6n-3) in the seston. The growth rate was overall higher for nauplii fed cultured microalgae compared to the nauplii fed natural seston. Although the nauplii fed algae cultures were fed surplus food, the growth did vary between the growth periods. Furthermore, the growth rate for nauplii fed natural seston and for nauplii fed cultured algae were positively related, suggesting that the maternal condition and the food quality experienced by the mothers could explain some of the variation in naupliar growth rate. We present lipid class data on Calanus finmarchicus eggs from field samples that, contrary to previous studies, showed a high content of wax esters. Fatty acid analyzes of eggs, nauplii stages and copepodites from field samples showed that eggs and nauplii have a similar fatty acid composition and that the main increase in the content and share of DHA and EPA was from nauplii to copepodite. The secondary production measured as naupliar growth was compared to the secondary production measured as carbon specific female egg production rate. The secondary production measured as egg production was generally higher than the secondary production measured as naupliar growth early in the spring, whereas the opposite situation was observed during post-bloom situations in late spring/early summer.
Emotion Analysis of Internet Chat

We present a system for Emotion Analysis of Instant Messages (IM). Using Instance Based classifier we have shown that our system can outperform similar systems in the IM domain. Tagged instant messages and elaborate feature engineering can help a lot in increasing the performance of text classification of unstructured, ungrammatical text. The impact of class imbalance on classification has been studied and demonstration has been made of how undersampling can help mitigate this problem.
Two New Rhabdoviruses (Rhabdoviridae) Isolated from Birds During Surveillance for Arboviral Encephalitis, Northeastern United States

Two novel rhabdoviruses were isolated from birds during surveillance for arboviral encephalitis in the northeastern United States. The first, designated Farmington virus, is a tentative new member of the Vesiculovirus genus. The second, designated Rhode Island virus, is unclassified antigenically, but its ultrastructure and size are more similar to those of some of the plant rhabdoviruses. Both viruses infect birds and mice, as well as monkey kidney cells in culture, but their importance for human health is unknown.
Dispersion-free operation in InAlN-based HEMTs with ultrathin or no passivation

The origin and management of DC-RF dispersion in InAlN-based GaN high electron mobility transistors (HEMTs) is examined, in conjunction with consideration of the implications for device speed. This study, in which GaN HEMTs with alloyed and non-alloyed ohmic contacts are compared, renders the following observations and hypotheses: 1) We show and explain that dispersion free operation can be achieved without passivation. 2) The root cause of dispersion associated with surface states is often introduced during device processing; in particular, unintentional or un-optimized oxidation of the HEMT surface. 3) These undesired surface states also lead to gate extension (virtual gate), which decreases device speed but increases the breakdown voltage. In addition, the function and efficacy of a plasma-based ultrathin passivation is evaluated.
Role of the Regulatory Gene rirA in the Transcriptional Response of Sinorhizobium meliloti to Iron Limitation

ABSTRACT A regulatory network of Sinorhizobium meliloti genes involved in adaptation to iron-limiting conditions and the involvement of the rhizobial iron regulator gene (rirA) were analyzed by mutation and microarray analyses. A constructed S. meliloti rirA mutant exhibited growth defects and enhanced H2O2 sensitivity in the presence of iron, but symbiotic nitrogen fixation was not affected. To identify iron-responsive and RirA-regulated S. meliloti genes, a transcriptome approach using whole-genome microarrays was used. Altogether, 45 genes were found to be jointly derepressed by mutation of rirA and under different iron-limited conditions. As expected, a number of genes involved in iron transport (e.g., hmuPSTU, shmR, rhbABCDEF, rhtX, and rhtA) and also genes with predicted functions in energy metabolism (e.g., fixN3, fixP3, and qxtAB) and exopolysaccharide production (e.g., exoY and exoN) were found in this group of genes. In addition, the iron deficiency response of S. meliloti also involved rirA-independent expression changes, including repression of the S. meliloti flagellar regulon. Finally, the RirA modulon also includes genes that are not iron responsive, including a gene cluster putatively involved in Fe-S cluster formation (sufA, sufS, sufD, sufC, and sufB).
Less hypoglycemia with insulin glargine in intensive insulin therapy for type 1 diabetes. U.S. Study Group of Insulin Glargine in Type 1 Diabetes.

OBJECTIVE Insulin glargine (21A-Gly-30Ba-L-Arg-30Bb-L-Arg-human insulin) is a biosynthetic insulin analog with a prolonged duration of action compared with NPH human insulin. This study compared insulin glargine with NPH human insulin in subjects with type 1 diabetes who had been previously treated with multiple daily injections of NPH insulin and regular insulin. RESEARCH DESIGN AND METHODS This study was a multicenter randomized parallel-group study in which subjects were randomized to receive premeal regular insulin and either insulin glargine (at bedtime) or NPH insulin (at bedtime for patients on once-daily therapy and at bedtime and in the morning for patients on twice-daily therapy) for up to 28 weeks. Dose titration of both basal insulins was based on capillary fasting whole blood glucose (FBG) levels; the goal was a premeal blood glucose concentration of 4.4-6.7 mmol/l. RESULTS A total of 534 well-controlled type 1 diabetic subjects (mean GHb 7.7%, mean fasting plasma glucose [FPG] 11.8 mmo/l) were treated. A small decrease in GHb levels was noted with both insulin glargine (-0.16%) and NPH insulin (-0.21%; P > 0.05). Significant reductions in median FPG levels from baseline (-1.67 vs. -0.33 mmol/l with NPH insulin, P = 0.0145) and a trend for a reduction in capillary FBG levels were achieved with insulin glargine. After the 1-month titration phase, significantly fewer subjects receiving insulin glargine experienced symptomatic hypoglycemia (39.9 vs. 49.2%, P = 0.0219) or nocturnal hypoglycemia (18.2 vs. 27.1%, P = 0.0116) with a blood glucose level <2.0 mmol/l compared with subjects receiving NPH insulin. CONCLUSIONS Lower FPG levels with fewer episodes of hypoglycemia were achieved with insulin glargine compared with once- or twice-daily NPH insulin as part of a basal-bolus regimen in patients with type 1 diabetes.
A Comparison of Two Commercial Volumetry Software Programs in the Analysis of Pulmonary Ground-Glass Nodules: Segmentation Capability and Measurement Accuracy

Objective To compare the segmentation capability of the 2 currently available commercial volumetry software programs with specific segmentation algorithms for pulmonary ground-glass nodules (GGNs) and to assess their measurement accuracy. Materials and Methods In this study, 55 patients with 66 GGNs underwent unenhanced low-dose CT. GGN segmentation was performed by using 2 volumetry software programs (LungCARE, Siemens Healthcare; LungVCAR, GE Healthcare). Successful nodule segmentation was assessed visually and morphologic features of GGNs were evaluated to determine factors affecting segmentation by both types of software. In addition, the measurement accuracy of the software programs was investigated by using an anthropomorphic chest phantom containing simulated GGNs. Results The successful nodule segmentation rate was significantly higher in LungCARE (90.9%) than in LungVCAR (72.7%) (p = 0.012). Vascular attachment was a negatively influencing morphologic feature of nodule segmentation for both software programs. As for measurement accuracy, mean relative volume measurement errors in nodules ≥ 10 mm were 14.89% with LungCARE and 19.96% with LungVCAR. The mean relative attenuation measurement errors in nodules ≥ 10 mm were 3.03% with LungCARE and 5.12% with LungVCAR. Conclusion LungCARE shows significantly higher segmentation success rates than LungVCAR. Measurement accuracy of volume and attenuation of GGNs is acceptable in GGNs ≥ 10 mm by both software programs.
An investigation into long-run abnormal returns using Propensity Score Matching

OF DISSERTATION AN INVESTIGATION INTO LONG-RUN ABNORMAL RETURNS USING PROPENSITY SCORE MATCHING This is a study in two parts. In part-1, I identify several methods of estimating long-run abnormal returns prevalent in the finance literature and present an alternative using propensity score matching. I first demonstrate the concept with a simple simulation using generated data. I then employ historical returns from CRSP and randomly select events from the dataset using various alternating criteria. I test the efficacy of different methods in terms of type-I and type-II errors in detecting abnormal returns over 1236and 60-month periods. I use various forms of propensity score matching: 1 – 5 Nearest Neighbors in Caliper using distance defined alternatively by Propensity Scores and the Mahalanobis Metric, and Caliper Matching. I show that overall, Propensity Score Matching with two nearest neighbors provides much better performance than traditional methods, especially when the occurence of events is dictated by the presence of certain firm characteristics. In part-2, I demonstrate an application of Propensity Score Matching in the context of open-market share repurchase announcements. I show that traditional methods are ill-suited for the calculation of long-run abnormal returns following such events. Consequently, I am able to improve upon such methods on two fronts. First, I improve upon traditional matching methods by providing better matches on multiple dimensions and by being able to retain a larger sample of firms from the dataset. Second, I am able to eliminate much of the bias inherent in the Fama-French type methods for this particular application. I show this using simulations on samples based on firms that resemble a typical repurchasing firm. As a result, I obtain a statistically significant 1-, 3-, and 5-year abnormal return of about 2%, 5%, and 10% respectively, which is much lower than what prior literature has shown using traditional methods. Further investigation revealed that much of these returns are unique to small and unprofitable firms.
Proton radiation effects on medium/large area Si PIN photodiodes for Optical Wireless Links for Intra-Satellite Communications (OWLS)

Components off the shelf (cots) photodiodes suitable for OWLS were irradiated with ~10 to ~60 MeV protons and up to fluences of ~2.5-1012 p/cm2. Electrical and optoelectronic parameters were measured during the test (I-V curves, dark current, responsivity and ideal diode factor). Results on degradation and post-annealing are reported. Preliminary results on the lattice effects are also pointed.
Cortical connections of the visuomotor parietooccipital area V6Ad of the macaque monkey

Area V6A, a functionally defined region in the anterior bank of the parietooccipital sulcus, has been subdivided into dorsal and ventral cytoarchitectonic fields (V6Ad and V6Av). The aim of this study was to define the cortical connections of the cytoarchitectonic field V6Ad. Retrograde and bidirectional neuronal tracers were injected into the dorsal part of the anterior bank of parietooccipital sulcus of seven macaque monkeys (Macaca fascicularis). The limits of injection sites were compared with those of cytoarchitectonic fields. The major connections of V6Ad were with areas of the superior parietal lobule. The densest labeling was observed in the medial intraparietal area (MIP). Areas PEc, PGm, and V6Av were also strongly connected. Labeled cells were found in medial parietal area 31; in cingulate area 23; in the anterior (AIP), ventral (VIP), and lateral (LIP) intraparietal areas; in the inferior parietal lobule (fields Opt and PG); and in the medial superior temporal area (MST). In the frontal lobe, the main projection originated from F2, although labeled cells were also found in F7 and area 46. Preliminary results obtained from injections in nearby areas PEc and V6Av revealed connections different from those of V6Ad. In agreement with functional data, the strong connections with areas where arm‐reaching activity is represented suggest that V6Ad is part of a parietofrontal circuit involved in the control of prehension, and connections with AIP specifically support an involvement in the control of grasping. Connections with areas LIP and Opt are likely related to the oculomotor activities observed in V6Ad. J. Comp. Neurol. 513:622–642, 2009. © 2009 Wiley‐Liss, Inc.
Landbird productivity in central coastal California: the relationship to annual rainfall and a reproductive failure in 1986

The avian productivity of 51 locally breeding species in coastal grassland, coastal scrub, and mixed evergreen forest habitats was estimated from 11 years of standardized mist-netting data collected between 10 May and 17 August at Point Reyes Bird Observatory’s Palomarin Field Station. A relationship between the number of young birds banded per 100 net hr and the amount of annual (winter) rainfall during the previous season was apparent for the 10 years 1976 to 1985: productivity was low (19 to 32% below the 1 Oyear mean) in years of extremely low rainfall, increased to a maximum (21 to 39% above the IO-year mean) in years of average or slightly above average rainfall, and decreased substantially (20% below the IO-year mean) in years of very heavy rainfall. The number of young birds banded per 100 net hr in 1986, however, was 62.3% below the previous loyear mean and fell well outside the above relationship. This high level of reproductive failure occurred in most of the 51 locally breeding species and was independent of migratory behavior, habitat choice, and nest location. It was not independent of foraging behavior, however, as swallows and woodpeckers, species that feed their young on insects produced in decomposeror detritus-based food chains rather than in primary production-based food chains, showed no significant reduction in productivity. Timing of the decrease in young birds suggests that the onset of reproductive failure occurred in mid-May, well after the nesting season began. Such a large-scale reproductive failure of virtually an entire landbird community has not been reported before and no obvious weather factors appear to explain it. Preliminary data indicate that the reproductive failure was not confined to the vicinity of Palomarin or to central coastal California but rather extended over much of northern California even to the west slope of the Sierra Nevada. It is interesting, but perhaps only coincidental, that several circumstances of this phenomenon, including its timing, appear to coincide remarkably well with the passage of a radioactive “cloud” from the Chernobyl nuclear power plant accident and associated rainfall.
The Small RNA DsrA Influences the Acid Tolerance Response and Virulence of Salmonella enterica Serovar Typhimurium

The Gram-negative, enteropathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) is exposed to various stress conditions during pathogenesis, of which acid stress serves as a major defense mechanism in the host. Such environments are encountered in the stomach and Salmonella containing vacuole of phagocytic and non-phagocytic cells. It is only recently that small RNAs (sRNAs) have come to the forefront as major regulators of stress response networks. Consequently, the sRNA DsrA which regulates acid resistance in Escherichia coli, has not been characterized in the acid tolerance response (ATR) of Salmonella. In this study, we show dsrA to be induced two and threefold under adaptation and challenge phases of the ATR, respectively. Additionally, an isogenic mutant lacking dsrA (ΔDsrA) displayed lower viability under the ATR along with reduced motility, feeble adhesion and defective invasion efficacy in vitro. Expression analysis revealed down regulation of several Salmonella pathogenicity island-1 (SPI-1) effectors in ΔDsrA compared to the wild-type, under SPI-1 inducing conditions. Additionally, our in vivo data revealed ΔDsrA to be unable to cause gut inflammation in C57BL/6 mice at 72 h post infection, although intracellular survival and systemic dissemination remained unaffected. A possible explanation may be the significantly reduced expression of flagellin structural genes fliC and fljB in ΔDsrA, which have been implicated as major proinflammatory determinants. This study serves to highlight the role of sRNAs such as DsrA in both acid tolerance and virulence of S. Typhimurium. Additionally the robust phenotype of non-invasiveness could be exploited in developing SPI-I attenuated S. Typhimurium strains without disrupting SPI-I genes.
Self-assessment : methods , management and process

Self-assessment is a method for reviewing the activities and performance of an organization. This paper reports the findings of a study in four organizations of their management of this process. Each company followed the key self-assessment stages of planning, developing awareness, implementation and review but carried out the process in a different manner. The level of total quality management (TQM) maturity, available resources and organizational culture were the main factors for the differences. The key to successful self-assessment is effective management and the use of a team to manage the process. The most important activities were identified as: selection of a suitable model, appropriate approach(es) for the assessment, provision of appropriate training, monitoring the progress of improvement actions, establishment of a 'closed-loop' structure for the improvement cycle and integration of improvement with the strategic business plan. It is also pointed out that self-assessment is not without difficulties, including scarcity of time, overemphasis on scoring and scores, failing to follow-up improvement actions and lack of communication.
Computing quadratic function fields with high 3-rank via cubic field tabulation

This paper presents an algorithm for generating all imaginary and unusual discriminants up to a fixed degree bound that define a quadratic function field of positive 3-rank. Our method makes use of function field adaptations of a method due to Belabas for finding quadratic number fields of high 3-rank and of a refined function field version of a theorem due to Hasse. We provide numerical data for discriminant degree up to 11 over the finite fields $\mathbb{F}_{5}, \mathbb{F}_{7}, \mathbb{F}_{11}$ and $\mathbb{F}_{13}$. A special feature of our technique is that it produces quadratic function fields of minimal genus for any given 3-rank. Taking advantage of certain $\mathbb{F}_{q}(t)$-automorphisms in conjunction with Horner's rule for evaluating polynomials significantly speeds up our algorithm in the imaginary case; this improvement is unique to function fields and does not apply to number field tabulation. These automorphisms also account for certain divisibility properties in the number of fields found with positive 3-rank. Our numerical data mostly agrees with the predicted heuristics of Friedman-Washington and partial results on the distribution of such values due to Ellenberg-Venkatesh-Westerland for quadratic function fields over the finite field $\finfldq{q}$ where $q \equiv -1 \pmod{3}$. The corresponding data for $q \equiv 1 \pmod{3}$ does not agree closely with the previously mentioned heuristics and results, but does agree more closely with some recent number field conjectures of Malle and some work in progress on proving such conjectures for function fields due to Garton.