Miracle-dz/UniFAR-FTUs huggingface dataset:
A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis

Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing -mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown) organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp. com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.
Effects of Foliar Herbivory by Insects on the Fitness of Raphanus raphanistrum: Damage Can Increase Male Fitness

Generally, effects of herbivory on plant fitness have been measured in terms of female reproductive success (seed production). However, male plant fitness, defined as the number of seeds sired by pollen, contributes half of the genes to the next generation and is therefore crucial to the evolution of natural plant populations. This is the first study to examine effects of insect herbivory on both male and female plant reproductive success. Through controlled field and greenhouse experiments and genetic paternity analysis, we found that foliar damage by insects caused a range of responses by plants. In one environment, damaged plants had greater success as male parents than undamaged plants. Neither effects on pollen competitive ability nor pollinator visitation patterns could explain the greater siring success of these damaged plants. Success of damaged plants as male parents appeared to be due primarily to changes in allocation to flowers versus seeds after damage. Damaged plants produced more flowers early in the season, but not more seeds, than undamaged plants. Based on total seed production, male fitness measures from the first third of the season, and flower production, we estimated that damaged and undamaged plants had equal total reproductive success at the end of the season in this environment. In a second, richer environment, damaged and undamaged plants had equal male and female plant fitness, and no traits differed significantly between the treatments. Equal total reproductive success may not be ecologically or evolutionarily equivalent if it is achieved differentially through male versus female fitness. Genes from damaged plants dispersed through pollen may escape attack from herbivores, if such attack is correlated spatially from year to year.
Comparative Analysis of Fecal Microbiota in Infants with and without Eczema

Eczema is a chronic form of childhood disorder that is gaining in prevalence in affluent societies. Previous studies hypothesized that the development of eczema is correlated with changes in microbial profile and composition of early life endemic microbiota, but contradictory conclusions were obtained, possibly due to the lack of minimization of apparent non-health related confounders (e.g., age, antibiotic consumption, diet and mode of delivery). In this study, we recruited seven caesarean-delivered and total formula-fed infants, and comparatively examined the early-life endemic microbiota in these infants with and without eczema. Using 16S pyrosequencing, infants' fecal microbiota were observed to comprise Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as the four main phyla, and the presence and absence of specific populations within these four phyla are primarily mediated by ageing. Quantitative analysis of bacterial targets on a larger sample size (n = 36 at 1, 3, and 12 months of age) revealed that the abundances of Bifidobacterium and Enterobacteriaceae were different among caesarean-delivered infants with and without eczema, and the bacterial targets may be potential biomarkers that can correlate to the health status of these infants. Our overall findings suggest that the minimization of possible confounders is essential prior to comparative evaluation and correlation of fecal microbiota to health status, and that stool samples collected from caesarean-delivered infants at less than 1 year of age may represent a good cohort to study for potential biomarkers that can distinguish infants with eczema from those without. These findings would greatly facilitate future efforts in understanding the possible pathogenesis behind certain bacterial targets, and may lead to a timely intervention that reduces the occurrence of early life eczema and possibly allergic disorders in later life.
Vma8p-GFP Fusions Can Be Functionally Incorporated into V-ATPase, Suggesting Structural Flexibility at the Top of V1

The vacuolar ATPase (V-ATPase) complex of yeast (Saccharomyces cerevisiae) is comprised of two sectors, V1 (catalytic) and VO (proton transfer). The hexameric (A3B3) cylinder of V1 has a central cavity that must accommodate at least part of the rotary stalk of V-ATPase, a key component of which is subunit D (Vma8p). Recent electron microscopy (EM) data for the prokaryote V-ATPase complex (Thermus thermophilus) suggest that subunit D penetrates deeply into the central cavity. The functional counterpart of subunit D in mitochondrial F1FO-ATP synthase, subunit γ, occupies almost the entire length of the central cavity. To test whether the structure of yeast Vma8p mirrors that of subunit γ, we probed the location of the C-terminus of Vma8p by attachment of a large protein adduct, green fluorescent protein (GFP). We found that truncated Vma8p proteins lacking up to 40 C-terminal residues fused to GFP can be incorporated into functional V-ATPase complexes, and are able to support cell growth under alkaline conditions. We conclude that large protein adducts can be accommodated at the top of the central cavity of V1 without compromising V-ATPase function, arguing for structural flexibility of the V1 sector.
Rab11 Regulates the Compartmentalization of Early Endosomes Required for Efficient Transport from Early Endosomes to the Trans-Golgi Network

Several GTPases of the Rab family, known to be regulators of membrane traffic between organelles, have been described and localized to various intracellular compartments. Rab11 has previously been reported to be associated with the pericentriolar recycling compartment, post-Golgi vesicles, and the trans-Golgi network (TGN). We compared the effect of overexpression of wild-type and mutant forms of Rab11 on the different intracellular transport steps in the endocytic/degradative and the biosynthetic/exocytic pathways in HeLa cells. We also studied transport from endosomes to the Golgi apparatus using the Shiga toxin B subunit (STxB) and TGN38 as reporter molecules. Overexpression of both Rab11 wild-type (Rab11wt) and mutants altered the localization of the transferrrin receptor (TfR), internalized Tf, the STxB, and TGN38. In cells overexpressing Rab11wt and in a GTPase-deficient Rab11 mutant (Rab11Q70L), these proteins were found in vesicles showing characteristics of sorting endosomes lacking cellubrevin (Cb). In contrast, they were redistributed into an extended tubular network, together with Cb, in cells overexpressing a dominant negative mutant of Rab11 (Rab11S25N). This tubularized compartment was not accessible to Tf internalized at temperatures <20°C, suggesting that it is of recycling endosomal origin. Overexpression of Rab11wt, Rab11Q70L, and Rab11S25N also inhibited STxB and TGN38 transport from endosomes to the TGN. These results suggest that Rab11 influences endosome to TGN trafficking primarily by regulating membrane distribution inside the early endosomal pathway.
Acoustic characteristics of vowels and plosives/affricates of Mandarin-speaking hearing-impaired children

This article presents the results of an acoustic analysis of vowels and plosives/affricates produced by 45 Mandarin-speaking children with hearing impairment. Vowel production is represented and categorized into three groups by vowel space size calculated with normalized F1 and F2 values of corner vowels. The correlation between speech intelligibility and language abilities assessed by the level of word comprehension and the complexity of sentence structure is statistically significant. Vowel space grouping is correlated with speech intelligibility and spike percentage of plosives/affricates production. The generalized linear model analysis also shows that the level of word comprehension and the degree of hearing loss are the two most significant factors in predicting speech intelligibility. The statistical results suggest that the interplay of acoustic characteristic and speech ability is complex.
Biliary Tract Complications after Liver Transplantation: A Review

Biliary complications continue to be a major cause of morbidity in liver transplant recipients with an incidence of 10–30% following whole-organ transplantation and a mortality rate of up to 10%. Biliary leaks and strictures are most common but sphincter of Oddi dysfunction, hemobilia, and biliary obstruction are also observed. Biliary complications may be related to various factors such as hepatic artery patency, preservation injury, cytomegalovirus infection, chronic ductopenic rejection, ABO incompatibility, and technical reasons. The latter include imperfect anastomosis, T-tube-related complications and the use of partial liver grafts when cut surface biliary leaks or inadvertent bile duct injuries may occur during parenchymal division. The usage of a T-tube for duct-to-duct anastomosis in whole-organ liver transplantation remains controversial, mainly because of the high rates of T-tube-related complications observed in many series. In this article we review the etiology, as well as the main types of biliary complications according to the technique of biliary reconstruction and liver transplant procedure performed. Their management is also discussed with interventional radiology and endoscopic techniques emerging as the preferred treatment option, obviating the need for surgery in a selected majority of patients.
Seam Tracking Monitoring Based on Adaptive Kalman Filter Embedded Elman Neural Network During High-Power Fiber Laser Welding

This paper proposes a method of seam tracking monitoring during high-power fiber laser welding. A visual sensor system was employed to capture the infrared images of molten pools and the surroundings in the laser welding process. A weld seam position variable was extracted by the image difference and centroid algorithms. The state and measurement equations for weld seam position were established based on an eigenvector derived from the weld seam position variable. A Sage-Husa adaptive Kalman filter (AKF), as an estimator of the noise statistical characteristics, was applied in order to enhance the filtering precision. By embedding an Elman neural network into the AKF, an error estimator was used to compensate for the filtering errors. The results of the welding experiments have demonstrated the effectiveness of the proposed method to improve the accuracy of weld detection.
Is There Functional Collateral Flow During Vascular Occlusion in Angiographically Normal Coronary Arteries?

Background—Thus far, it is unknown whether there is functional collateral flow through preexisting anastomoses in patients with angiographically normal coronary arteries. Such preformed coronary collateral vessels could form the basis for subsequently developing protective natural bypasses in the presence of coronary artery disease. Methods and Results—Among 100 patients, the collateral flow index (CFI) was measured in coronary arteries without stenotic lesions. The CFI was determined by simultaneous measurement of mean aortic pressure, central venous pressure, and coronary wedge pressure via a sensor-tipped guidewire at the end of a 1-minute balloon occlusion. Patients were divided in 2 groups according to complete angiographic absence (51 patients) or partial presence (49 patients) of stenotic lesions in coronary arteries other than that undergoing collateral measurement. CFI in all patients (61±10 years; men/women, 69/31) amounted to 0.18±0.08 (range, 0.04 to 0.36). It showed a normal Gaussian frequency distribution; 22 individuals had a CFI ≥0.25, a value that was empirically found to represent well-developed collaterals protective against myocardial ischemia during coronary occlusion. Accordingly, 17 patients did not reveal signs of myocardial ischemia during coronary balloon occlusion, as assessed from an intracoronary ECG, and 26 patients did not experience angina pectoris during occlusion. Conclusion—In humans with angiographically normal coronary arteries, there are functional collateral vessels to the extent that one fifth to one quarter of them do not show signs of myocardial ischemia during brief vascular occlusions.
New classification for probe-based confocal laser endomicroscopy in the colon

Background and aims: Probe-based confocal laser endomicroscopy (pCLE; Cellvizio, Mauna Kea Technologies, Paris, France) enables in vivo histology during colonoscopy and may allow endoscopists to make real-time diagnoses. A collaboration of five experts proposed a new pCLE classification for colonic use. The aim of this study was to assess interobserver agreement and accuracy of the new pCLE classification in the colon. Patients and methods: Eligible patients were prospectively investigated by pCLE. A subset of 13 pCLE video sequences was reviewed post hoc for the establishment of a new classification, which comprised three vessel categories and seven crypt categories. All five blinded observers then scored another set of 102 video sequences, using the new classification. Histopathology was used as a reference standard. Results: The interobserver agreements on vessel and crypt architecture were ‘fair’ with kappa values of 0.29 and 0.27, respectively. When the classification was reduced to neoplasia vs. non-neoplasia (i. e. vessel or crypt type 3), overall agreement became ‘moderate’ (κ = 0.56). Overall sensitivity and specificity for predicting neoplasia was 66 % and 83 %, respectively. When all observers agreed (69 % of videos), the corresponding figures became 80 % and 95 %. Conclusion: A new classification for pCLE in the colon had a ‘moderate’ interobserver agreement for differentiating neoplasia from non-neoplastic tissue in the colon. The overall accuracy (81 %) for predicting neoplasia was acceptable and became excellent (94 %) when all five observers agreed. Future research should focus on refinement and validation of the classification.
Measuring renal blood flow in acute kidney injury: finally putting the horse before the cart.

Crit Care Med 2012 Vol. 40, No. 6 5. Bellomo R, Cass A, Cole L, et al: An observational study fluid balance and patient outcomes in the randomized evaluation of normal vs. augmented level of replacement therapy trial. Crit Care Med 2012; 40:1753–1760 6. Rivers E, Nguyen B, Havstad S, et al; Early Goal-Directed Therapy Collaborative Group: Early goal-directed therapy in the treatment of severe sepsis and septic shock. N Engl J Med 2001; 345: 1368–1377 7. Prowle JR, Echeverri JE, Ligabo EV, et al: Fluid balance and acute kidney injury. Nat Rev Nephrol 2010; 6:107–115 8. Kellum JA: Impaired renal blood flow and the ‘spicy food’ hypothesis of acute kidney injury. Crit Care Med 2011; 39:901–903 9. Rachoin JS, Kellum JA: Timing of fluid administration in critically ill patients with acute kidney injury: Every good thing has an end. Crit Care Med 2011; 39:2766–2767
Grace's Inheritance

This article is an apologia for the design of inheritance in the Grace educational programming language: it explains how the design of Grace’s inheritance draws from inheritance mechanisms in predecessor languages, and defends that design as the best of the available alternatives. For simplicity, Grace objects are generated from object constructors, like those of Emerald, Lua, and Javascript; for familiarity, the language also provides classes and inheritance, like Simula, Smalltalk and Java. The design question we address is whether or not object constructors can provide an inheritance semantics similar to classes.
A Role for Nrf2 in Redox Signalling of the Invasive Extravillous Trophoblast in Severe Early Onset IUGR Associated with Preeclampsia

Background Preeclampsia (PE) is characterized by increased lipid oxidation and diminished antioxidant capacity, while intrauterine growth restriction (IUGR) is characterized by impaired invasion of the extravillous trophoblast. Vascular endothelial growth factor (VEGF) has been reported to be altered in preeclampsia. A relationship between VEGF and nuclear factor erythroid 2-related factor-2 (Nrf2) has been shown in vitro, where VEGF prevents oxidative damage via activation of the Nrf2 pathway. In this study the expression of Nrf2, VEGF and 4-hydroxynonenal (4-HNE), was determined in interstitial and endovascular/intramural extravillous trophoblast (EVT) in normal pregnancies and those complicated by severe early onset IUGR associated with preeclampsia IUGR/PE. Materials and Methods Full-thickness uterine tissues derived from caesarean hysterectomies performed in 5 healthy normotensive women delivering term infants and 6 women with severe early onset IUGR with preeclampsia (29–34 weeks gestation) were analyzed. Interstitial and endovascular extravillous trophoblast were quantified after immunohistochemical staining of paraffin sections using antibodies against Nrf2, 4-HNE, VEGF, and cytokeratin 7. Results Uterine tissues from women suffering from severe early onset IUGR/PE were characterized by reduced invasion of extravillous trophoblast into the endometrial and myometrial segments of spiral arteries in the placental bed. Extravillous trophoblast showed an increased cytoplasmic expression of Nrf2 and 4-HNE in IUGR/PE cases. The increased expression of Nrf2 in cases of IUGR/PE was associated with decreased expression of VEGF in these cells compared to controls. Conclusion Our data suggests that besides villous cytotrophoblast, also the extravillous trophoblast is a source of Nrf2-dependent genes. VEGF deficiency may cause higher oxidative stress in extravillous trophoblast in cases with IUGR/PE. The resulting reduced basal defence against oxidative stress and the higher vulnerability to oxidative damage may play a role in the limited trophoblast invasion into spiral arteries in cases suffering from severe early onset IUGR/PE.
Survival Benefits of Statins for Primary Prevention: A Cohort Study

Objectives Estimate the effect of statin prescription on mortality in the population of England and Wales with no previous history of cardiovascular disease. Methods Primary care records from The Health Improvement Network 1987–2011 were used. Four cohorts of participants aged 60, 65, 70, or 75 years at baseline included 118,700, 199,574, 247,149, and 194,085 participants; and 1.4, 1.9, 1.8, and 1.1 million person-years of data, respectively. The exposure was any statin prescription at any time before the participant reached the baseline age (60, 65, 70 or 75) and the outcome was all-cause mortality at any age above the baseline age. The hazard of mortality associated with statin prescription was calculated by Cox’s proportional hazard regressions, adjusted for sex, year of birth, socioeconomic status, diabetes, antihypertensive medication, hypercholesterolaemia, body mass index, smoking status, and general practice. Participants were grouped by QRISK2 baseline risk of a first cardiovascular event in the next ten years of <10%, 10–19%, or ≥20%. Results There was no reduction in all-cause mortality for statin prescription initiated in participants with a QRISK2 score <10% at any baseline age, or in participants aged 60 at baseline in any risk group. Mortality was lower in participants with a QRISK2 score ≥20% if statin prescription had been initiated by age 65 (adjusted hazard ratio (HR) 0.86 (0.79–0.94)), 70 (HR 0.83 (0.79–0.88)), or 75 (HR 0.82 (0.79–0.86)). Mortality reduction was uncertain with a QRISK2 score of 10–19%: the HR was 1.00 (0.91–1.11) for statin prescription by age 65, 0.89 (0.81–0.99) by age 70, or 0.79 (0.52–1.19) by age 75. Conclusions The current internationally recommended thresholds for statin therapy for primary prevention of cardiovascular disease in routine practice may be too low and may lead to overtreatment of younger people and those at low risk.
Plant populations and chemical weed control in soybean cross-sowing

Authors declare no conflict of interest In soybean production in Brazil, the ends often justify the means. The high marketing prices of grains have motivated producers to adopt new techniques for cultivation of the legume in an empirical way or without adequate scientific support. Thus, we hypothesized that soybean cross-sowing in equal populations or twice (as used in conventional sowing in parallel rows) may increase soybean yield and decrease weed infestation in crops. In this study, we aimed to evaluate the spatial arrangements of plants associated with the presence or absence of chemical treatment for weed control in the soybean crop. A randomized block design was used with five treatments (four replicates per treatment): 1) uncrossed with the recommended plant population; 2) crossed with the recommended plant population; 3) crossed with double the plant population; 4) crossed with the same plant population and without herbicide; and 5) crossed with double the plant population and without herbicide. Soybeans cross-sowed with the recommended plant population had the same growth as uncrossed soybeans in terms of height and dry matter of shoot and roots, but had a higher leaf area index. Moreover, root nodulation increased in number with soybeans cross-sowed with the recommended plant population and in mass for soybeans cross-sowed with double the plant population, without differences in indirect measures of chlorophyll. Thus, our findings suggested that crosssowing with the recommended plant population or double the recommended plant population did not aid in weed control and did not increase the yield of soybean grains.