Miracle-dz/UniFAR-FTUs huggingface dataset:
Stirring up Development with the Heterotrimeric Kinesin KIF3

KIF3 is a heterotrimeric member of the kinesin superfamily of microtubule associated motors. This functionally diverse family of motors is involved in anterograde transport of membrane bound organelles in neurons and melanosomes, mediates transport between the endoplasmic reticulum and the Golgi, and transports protein complexes within cilia and flagella required for their morphogenesis. Interestingly, a mutation of KIF3, which impairs ciliogenesis in nodal cells, prevents the unidirectional leftward flow (nodal flow) of putative morphogens during embryogenesis, thereby altering the development of left–right asymmetry in mammals.
How Does Bug-Handling Effort Differ Among Different Programming Languages?

Handling bugs is an essential part of software development. The impact of programming language on this task has long been a topic of much debate. For example, some people hold the view that bugs in Python are easy to handle because its code is easy to read and understand, while some others believe the absence of static typing in Python will lead to higher bug-handling effort. This paper presents the first large-scale study to investigate whether the ecosystems of different (categories of) programming language would require different bug-handling effort. The focus is on correlation analysis rather than causal analysis. With 600 most popular projects in 10 languages downloaded from GitHub (summing up to 70,816,938 SLOC and 3,096,009 commits), the experimental results indicate various interesting findings. First, different languages require different bug-handling effort. For example, Java and C# tend to require less time but more line/file modification, Python and PHP tend to require less time and less line/file modification, while Ruby and JavaScript tend to require more time as well as more line/file modification. Second, weak/dynamic languages tend to require more time than strong/static languages, while static languages tend to require more absolute line/file modification. A toy predictive model also provides proof that the inclusion of programming languages could improve the effectiveness when predicting the bug-handling effort of a project.
In vitro determination of ruminal protein degradability using [15N]ammonia to correct for microbial nitrogen uptake.

An in vitro procedure was developed to estimate rate and extent of ruminal protein degradation using [15N]H3 to quantify uptake of protein degradation products for microbial protein synthesis. Incubations were conducted for 6 h in stirrer flasks with ruminal inoculum plus buffer, reducing solution, pectin, soluble carbohydrates, and added (15NH4)2SO4. Seven protein concentrates were tested in the system. Samples of media were analyzed for 15N enrichment of NH3, microbial N, and total solids N. Degradation rate was computed from net (i.e., protein-added minus blank) release of NH3 N plus net synthesis of microbial protein N; escape was estimated assuming ruminal passage rate = . 06/h. Over the course of the incubations, pH was stable at 6.6, protozoal numbers increased slightly, and microbial protein content increased by more than 200%. Free AA had not accumulated at the end of the incubations. Microbial protein synthesis was a linear function (P < .001; r2 = .780) of extent of degradation. Mean degradation rates and ruminal escapes determined were, respectively, . 569/h and 10% (casein), . 148/h and 29% (solvent soybean meal), . 036/h and 63% (expeller soybean meal), . 026/h and 70% (low solubles fish meal), . 063/h and 49% (high solubles fish meal), . 034/h and 64% (corn gluten meal), and . 050/h and 55% (roasted soybeans). Overall, degradation rates averaged 28% greater than those previously estimated using an inhibitor in vitro system; however, rates obtained for the fish meals using the 15N method were slower.
Non-Market Measurement Techniques of Willingness to Pay, the Case of Environmental Resources: A Review

The objective of this study is to review measurement techniques of willingness to pay (WTP), comparison of techniques and review of empirical evidences to support the theoretical concept of willingness to pay measurement methods. Particularly, the review mainly focuses on stated preference method. To address these objectives, intensive literature review was under taken. Finally, the result of the review was presented in narration, tabular and diagrammatic form. The review indicated that the concept of WTP has been applied in different field of study to assign monetary value using observed market behavior and hypothetical market scenarios for non-marketed goods and services. There are two commonly used methods for estimating WTP into revealed and stated preference methods. Depending on the type of goods or services in question, the time and research resources available, both methods can be useful though they have their own advantages and disadvantages. Revealed preference technique is used to estimate the use value only; on the other hand, stated preference technique is applicable to estimate both use and non-use value. This indicates that stated preference technique has broader scope than revealed preference.
Cellular Epigenetic Modifications of Neural Stem Cell Differentiation

Emerging information indicates that epigenetic modification (i.e., histone code and DNA methylation) may be integral to the maintenance and differentiation of neural stem cells (NSCs), but their actual involvement has not yet been illustrated. In this study, we demonstrated the dynamic nature of epigenetic marks during the differentiation of quiescent adult rat NSCs in neurospheres. A subpopulation of OCT4+ NSCs in the neurosphere contained histone marks, trimethylated histone 3 on lysine 27 (3me-H3K27), 2me-H3K4, and acetylated H4 (Ac-H4). A major decrease of these marks was found prior to or during differentiation, and was further diminished or reprogrammed in diverse subpopulations of migrated NSCs expressing nestin or β-III-tubulin. The DNA methylation mark 5-methyl-cytosine (5-MeC), and DNA methyltransferase (DNMT) 1 and 3a expression also correlated to the state of differentiation; they were highly present in undifferentiated NSCs but downregulated in migrated populations. In contrast, DNA methyl-CpG-binding protein (MBD1) was low in undifferentiated NSCs in neurospheres, but highly appeared in differentiating NSCs. Furthermore, we found an outward translocation of DNA methylation marker 5-MeC, DNMT1, DNMT3a, and MBD1 in NSCs as differentiation began and proceeded; 5-MeC from homogeneous nucleus to peripheral nucleus, and DMNT1a and 3a from nuclear to cytoplasm, indicating chromatin remodeling. Treatment with DNA methylation inhibitor, 5-aza-cytidine, altered DNA methylation and disrupted migration as indicated by a reduction of migrated neurons and differentiation. These results indicate that chromatin is dynamically remodeled when NSCs transform from the quiescent state to active growth, and that DNA methylation modification is essential for neural stem cell differentiation.
Performance Characteristics of Seven Nutrition Label Formats

The authors evaluate seven nutrition label formats to determine consumer comprehension and acceptance of displayed information. They test comprehension on five tasks: comparing two products, judging healthfulness, verifying claims, estimating servings needed to meet the daily requirement for a nutrient, and balancing nutrients in a daily diet. Performance scores were higher on some tasks—particularly dietary management ones—for formats that displayed nutrient amounts in percentages than for those that displayed nutrient amounts in metric units, even when interpretational aids were included on the metric formats. The two most preferred formats were metric formats with an interpretational aid. The findings have an important impact on decisions about the final nutrition label format required by the Food and Drug Administration.
Is Information Enough? The Effect of Information about Education Tax Benefits on Student Outcomes

There is increasing evidence that tax benefits for college do not affect college enrollment. This may be because prospective students do not know about tax benefits for college or because the design of tax benefits is not conducive to affecting educational outcomes. We focus on changing awareness of tax benefits by providing information to students or prospective students. We sent e-mails and letters to students that described tax benefits for college and tracked college outcomes. For all three of our samples—rising high school seniors, already enrolled students, and students who had previously applied to college but were not currently enrolled—information about tax benefits for college did not affect enrollment or reenrollment. We test whether effects vary according to information frames and found that no treatment arms changed student outcomes. We conclude that awareness is not the primary reason that tax benefits for college do not affect enrollment. ∗Teachers College, Columbia University. bergman@tc.columbia. edu. The authors would like to thank the Texas Higher Education Coordinating Board for providing the data and invaluable assistance. We also acknowledge funding from JPAL–North America and the UT–Austin Population Research Center. The conclusions of this research do not necessarily reflect the opinion or official position of the Texas Higher Education Coordinating Board. All errors are our own. †Brigham Young University and IZA, jeffdenning@byu.edu ‡University of Texas at Austin and NBER, dsmanoli@austin.utexas. edu
Biology and Clinical Applications of Longterm Bone Marrow Cultures

A number of clonogenic assays for short-term bone marrow culture is now available for the quantitative analysis of the various hematopoietic progenitor cell classes. The short-term assays are not suitable to analyse either stem cell selfrenewal or interactions of hematopoietic progenitors with stromal cells, especially those requiring direct cell-to-cell or cell-to-matrix contact. The technique of longterm bone marrow culture (LTBMC) allows a sustained production of myeloid cells when marrow is placed in liquid culture at relatively high cell concentration, with appropriate supplements, temperature and feeding conditions. A peculiar feature of LTBMC is that the stromal cells promote selfrenewal as well as differentiation of the stem cells, without the need to add exogenous growth factors. The LTBMC system offers an approach able to investigate not only the proliferative and differentiative events but also sustained cell production and selfrenewal of any clonogenic cell types. In the last years, the technique of LTBMC has been increasingly used by several groups to investigate hematopoietic regulation, stromal cell function and the interactions among stromal and hematopoietic cells. In the present report, the biology of LTBMC and their possible clinical applications will be reviewed.
Fast algorithms for topk personalized pagerank queries

In entity-relation (ER) graphs (V,E), nodes V represent typed entities and edges E represent typed relations. For dynamic personalized PageRank queries, nodes are ranked by their steady-state probabilities obtained using the standard random surfer model. In this work, we propose a framework to answer top-k graph conductance queries. Our top-k ranking technique leads to a 4X speedup, and overall, our system executes queries 200-1600X faster than whole-graph PageRank. Some queries might contain hard predicates i.e. predicates that must be satisfied by the answer nodes. E.g. we may seek authoritative papers on public key cryptography, but only those written during 1997. We extend our system to handle hard predicates. Our system achieves these substantial query speedups while consuming only 10-20% of the space taken by a regular text index.
Effect of Duplicate Isolates of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus on Antibiogram Data

ABSTRACT Duplicate Staphylococcus aureus isolates were analyzed to determine the impact of multiple isolates from the same patient on annual antibiogram data. During a 6-year period (1996 to 2001), 3,227 patients with 4,844 S. aureus isolates were evaluated. A total of 39% of patients with methicillin-resistant S. aureus (MRSA) (n = 860) and 23% of patients with methicillin-susceptible S. aureus (MSSA) (n = 2,367) infections had duplicate isolates. Cumulative data show that 91% of the patients during this 6-year period with duplicate isolates (2 to 13 duplicates/year) did not switch between MSSA and MRSA but retained the original S. aureus strain whether it was MSSA or MRSA. Rates of MRSA were calculated for each year by using all isolates and then eliminating duplicates. The impact of duplicate MRSA and MSSA isolates was evaluated by using the ratio of isolates per patient such that ratios of >1.0 indicate >1 isolate per patient. The 6-year ratio for MRSA was 1.90 isolates/patient, and the ratio for MSSA was 1.35. A significant difference (P < 0.05) was noted in the MRSA rates in 4 of 6 years when duplicate isolates were removed. Common phenotypic antibiogram patterns were compared for all MRSA isolates during the 6-year period, and 64% were of a single antibiogram phenotype. Eighty-eight percent of patients with duplicate MRSA isolates had phenotypically identical multiple isolates. The rate of MRSA differs when duplicate isolates are removed from the antibiogram data.
Interaction of Treponema pallidum (Nichols strain) with cultured mammalian cells: effects of oxygen, reducing agents, serum supplements, and different cell types

Cultured mammalian cells extend the time of survival of Treponema pallidum (Nichols strain). Various parameters that have been previously shown to enhance treponemal survival in vitro were examined for influences on the interaction of T. pallidum with cultured cells. With cells derived from normal rabbit testes, the time of retention of treponemal virulence was extended in an atmosphere containing reduced concentrations of oxygen. Glutathione and cysteine, when added to the basal tissue culture medium, prolonged treponemal survival. In an assessment of various tissue culture medium supplements, normal rabbit serum was equivalent to fetal bovine serum and superior to bovine serum albumin fraction V (BSA), fatty acid-poor BSA, and lipid-pooed for TRK-2, HSE, NRK, and C6 cells. Dithiotreitol, as an additional reducing agent, sharply enhanced treponemal survival. With SF1Ep NBL-11 cells and basal tissue culture medium containing glutathione, cysteine, and dithiothreitol, in an atmosphere of approximately 3% oxygen, T. pallidum was maintained without detectable decreases in the number of virulent organisms for 6 days.
"I Tremble for My Country": Thomas Jefferson and the Virginia Gentry

Hatzenbuehler argues that Jefferson, though celebrated as a nationalist, is best understood as a member of the Virginia gentry who viewed the nation through the lens of his native "country," the Commonwealth of Virginia. Throughout his life, Jefferson was torn between his participation in a privileged order and his periodic dissent from the order's ways. In taking Virginians to task for their failure to improve Virginia society, he masked his own reluctance to make fundamental changes in his life. The zenith of Jefferson's criticism came in Notes on the State of Virginia, where he chided his fellow Virginians for failing to take advantage of the opportunities that independence from Great Britain promised - including writing a new state constitution, establishing religious freedom, educating all of the state's youth, farming grains instead of planting tobacco, and abolishing slavery. The height of his withdrawal from the commitment to the change he advocated came after his presidency, when he allowed his gentry culture to ensnare him. The author also investigates specific issues of contention in the Jefferson literature, among them Jefferson's reliance on the writings of early Virginian writers and George Mason in drafting Summary View of the Rights of British America and the Declaration of Independence, the influence of the great French Encyclopedie on his composition of Notes on the State of Virginia, his authorship of the Kentucky Resolutions, his unfulfilled revolution as president, and the timing of the creation of the University of Virginia. Carefully drawing on Jefferson's voluminous correspondence, Hatzenbuehler does not shy away from the Founding Father's failings but finds much to admire.
A viral protein inhibits the long range signaling activity of the gene silencing signal

Post‐transcriptional gene silencing (PTGS) provides protection against viruses in plants by homology‐dependent RNA degradation. PTGS initiated locally produces a mobile signal that instructs specific RNA degradation at a distance. Here we show that this signal‐mediated intercellular spread of PTGS does not occur after PTGS initiation in cells expressing cucumber mosaic virus 2b protein (Cmv2b), a nucleus‐localized plant viral PTGS suppressor. Silencing spread via the signal was also effectively blocked in independent assays by expressing Cmv2b only in tissues through which the signal must travel to induce PTGS in the target cells. Furthermore, the signal imported externally into the Cmv2b‐expressing cells was not active in triggering degradation of the target RNA and loss of signal activity in these cells was associated with a significantly reduced transgene DNA methylation. These findings indicate that Cmv2b inhibits the activity of the mobile signal and interferes with DNA methylation in the nucleus. Signal inactivation provides a mechanistic basis for the known role of Cmv2b in facilitating virus spread to tissues outside of the primarily infected sites.
Inflammation links excess fat to insulin resistance: the role of the interleukin‐1 family

A growing body of evidence suggests that cytokines of the interleukin‐1 (IL‐1) family, particularly IL‐1β but also IL‐1Ra and IL‐18, are involved in obesity‐associated inflammation. IL‐1β is produced via cleavage of pro‐IL‐1β by caspase‐1, which in turn is activated by a multiprotein complex called the inflammasome. The components of the NLRP3 inflammasome are involved in sensing obesity‐associated danger signals, both in mice and in human (obese) subjects, with caspase‐1 seemingly the most crucial regulator. Autophagy is upregulated in obesity and may function as a mechanism to control IL‐1β gene expression in adipose tissue to mitigate chronic inflammation. All these mechanisms are operative in human adipose tissue and appear to be more pronounced in human visceral compared to subcutaneous tissue. In animal studies, blocking caspase‐1 activity results in decreased weight gain, decreased inflammation, and improved insulin sensitivity. Human intervention studies with IL‐1Ra (anakinra) have reported beneficial effects in patients with diabetes, yet without significant changes in insulin sensitivity. Clearly, the IL‐1 family of cytokines, especially IL‐1β, plays an important role in obesity‐associated inflammation and insulin resistance and may represent a therapeutic target to reverse the detrimental metabolic consequences of obesity.
Controller design and experimental validation of a robot joint with active compliance

The design employs direct drive torque motor to achieve a robot single joint with active compliance based on the impedance model. In order to maximize the torque density, transmission transparency and backdrivability, the joint employs a quasi-direct actuator that a single-stage planetary gear is mounted on the motor's rotor. When robot interacts with environments, it's inevitable to change the stiffness and damping coefficient of the joint. In view of the situation, a simple and efficient method-fuzzy control is employed and the effectiveness of the controller is verified experimentally. Finally, according to the algorithm of the outer loop position and inner loop force control, the position control of single joint is realized, and the dynamic response of the joint to the given sine position is tested experimentally.
Perinatal Undernutrition Modifies Cell Proliferation and Brain‐Derived Neurotrophic Factor Levels During Critical Time‐Windows for Hypothalamic and Hippocampal Development in the Male Rat

Maternal perinatal undernutrition (MPU) modifies the activity of the hypothalamic‐pituitary‐adrenal axis and sensitises to the development of metabolic and cognitive adult diseases. Because the hypothalamus and hippocampus are involved in the regulation of neuroendocrine activity, energy metabolism and cognition, we hypothesised that a maternal 50% food restriction (FR50) from day 14 of pregnancy (E14) until postnatal day 21 (P21) would affect the development of these structures in male rat offspring. Protein and mRNA levels of brain‐derived neurotrophic factor (BDNF) and cell proliferation [analysed by 5‐bromodeoxyuridine (BrdU) incorporation] were compared in both control and FR50 rats from E21 to P22. Although the pattern of the evolution of BDNF concentration and cell proliferation throughout development was not strikingly different between groups, several disturbances at specific developmental stages were observed. FR50 rats exhibited a delayed increase of hippocampal BDNF content whereas, in the hypothalamus, BDNF level was augmented from E21 to P14 and associated, at this latter stage, with an increased mRNA expression of TRkB‐T2. In both groups, a correlation between BDNF content and the number of BrdU positive cells was noted in the dentate gyrus, whereas opposite variations were observed in CA1, CA2 and CA3 layers, and in the arcuate and ventromedial nuclei. In the hippocampus, P15‐FR50 rats showed an increased number of BrdU positive cells in all regions, whereas, at P22, a decrease was observed in the CA2. In the hypothalamus, between E21 and P8, MPU increases the number of BrdU positive cells in all regions analysed and, until P15, marked differences were noticed in the median eminence, the paraventricular nucleus and the arcuate nucleus. Taken together, the results obtained in the present study show that MPU changes the time course of production of BDNF and cell proliferation in specific hippocampal and hypothalamic areas during sensitive developmental windows, suggesting that these early perinatal modifications may have long‐lasting consequences.
Lifestyle-related factors associated with successful weight loss

Abstract Background. Short-term weight loss is often successful, but the obtained results are difficult to maintain. Therefore, a study focusing on obese people who successfully lost weight, with special emphasis upon methods applied and background factors, is of major importance. Methods/subjects. This study was based upon a web-based questionnaire, which the participants filled in after registration. Altogether 316 people were recruited through articles in newspapers all over Finland, and of them 184 met the inclusion criteria: age 18–60 years, body mass index (BMI) ≥ 30 kg/m2 before weight loss, a weight loss of at least 10%, and maintaining it for a minimum of 2 years. Results. A total of 158 participants (100 women and 58 men) were included in the final analyses. The mean age was 44.5 years, average BMI before weight loss 35.9 kg/m2 and after weight loss 26.1 kg/m2, average weight loss was 26.5% or 32.4 kg. Compared with the general Finnish population the participants smoked less (P = 0.009), used less alcohol (P ≤ 0.001), and were physically more active (P ≤ 0.001). Conclusions. People who were successful in long-term weight loss have a much healthier lifestyle than the general Finnish population. Increased physical activity seems to be a major determinant of successful long-term results.