Miracle-dz/UniFAR-FTUs huggingface dataset:
BTWorld: towards observing the global BitTorrent file-sharing network

Today, the BitTorrent Peer-to-Peer file-sharing network is one of the largest Internet applications---it generates massive traffic volumes, it is deployed in thousands of independent communities, and it serves millions of unique users worldwide. Despite a large number of empirical and theoretical studies, observing the state of the global BitTorrent network remains a grand challenge for the BitTorrent community. To address this challenge, in this work we introduce BT-World, an architecture for observing the global BitTorrent network without help from the ISPs. We design BTWorld around three main features specific to BitTorrent measurements. First, our architecture is able to find public trackers, that is, the BitTorrent components that offer unrestricted service to peers around the world. Second, by observing the state of these trackers, BTWorld obtains information about the performance, scalability, and reliability of BitTorrent. Third, BTWorld is designed to pre-process the large volumes of recorded data for later analysis. We demonstrate the viability of our architecture by deploying it in practice, to observe and analyze one week of operation of a large part of the global BitTorrent network--over 10 million swarms and tens of millions of concurrent users. We also show that BT-World can shed light on BitTorrent phenomena, such as the presence of spam trackers and giant swarms.
Biochemical basis for dominant mutations in the Saccaromyces cerevisiae Msh6 gene

Errors that occur during DNA replication result in base‐base mismatches and small insertion/deletion mispairs that are usually corrected by the DNA mismatch repair (MMR) system. Defects in this highly conserved system lead to increased mutation rates, and in humans, result in increased development of cancer. In Eukaryotic cells, two different heterodimeric complexes, called Msh2‐Msh6 and Msh2‐Msh3, recognize base‐base mispairs and insertion/deletion mispairs. A previous study described four dominant msh6 mutations that interfere with the function of both Msh2‐Msh6 and Msh2‐Msh3‐dependent MMR. Initial biochemical studies showed that all of the dominant mutant Msh2‐Msh6 complexes had altered ATPase activity and three of the dominant mutant complexes had reduced ATP‐induced dissociation off of mispaired bases. Here, a detailed biochemical analysis of these mutant Msh2‐Msh6 complexes further examined the ATP‐binding and ATP hydrolysis properties as well as examined the ability of these proteins to function in downstream MMR events, including the ability to form sliding clamps and interact with the Mlh1‐Pms1 complex. The results revealed two mechanisms for dominance. In the first, the mutant Msh2‐Msh6 complex can bind the mispaired base, but is defective for the ATP‐induced sliding clamp formation and assembly of ternary complexes with Mlh1‐Pms1, and occludes the mispaired base from functional Msh complexes. In the second, the mutant complex can bind the mispaired base, is defective for ATP‐induced sliding clamp formation, but retains the ability to interact with Mlh1‐Pms1. In this latter case, either the mispair base is occluded or Mlh1‐Pms1 is sequestered and not available to act in alternate MMR pathways.
GENETIC POPULATION STRUCTURE OF DROSOPHILA TRIPUNCTATA: PATTERNS OF VARIATION AND COVARIATION OF TRAITS AFFECTING RESOURCE USE

Drosophila tripunctata is an ecological generalist, using both fruits and mushrooms as breeding sites. Isofemale strains of this species were established from seven populations over a wide part of its range and assayed for electrophoretic variability, oviposition‐site preference, and larval performance on several types of substrates. Significant variation among strains within populations was found for oviposition‐site preference, larval development time on tomatoes versus mushrooms, and tolerance (as measured by development time) of the mushroom toxin α‐amanitin. Even populations at the periphery of the range, which electrophoretic data suggest have been through bottlenecks, harbored levels of variation for oviposition‐site preference approximately equal to that found in central populations.
Perioperative Standard Oral Nutrition Supplements Versus Immunonutrition in Patients Undergoing Colorectal Resection in an Enhanced Recovery (ERAS) Protocol

AbstractTo compare immunonutrition versus standard high calorie nutrition in patients undergoing elective colorectal resection within an Enhanced Recovery After Surgery (ERAS) program.Despite progress in recent years in the surgical management of patients with colorectal cancer (ERAS programs), postoperative complications are frequent. Nutritional supplements enriched with immunonutrients have recently been introduced into clinical practice. However, the extent to which the combination of ERAS protocols and immunonutrition benefits patients undergoing colorectal cancer surgery is unknown.The SONVI study is a prospective, multicenter, randomized trial with 2 parallel treatment groups receiving either the study product (an immune-enhancing feed) or the control supplement (a hypercaloric hypernitrogenous supplement) for 7 days before colorectal resection and 5 days postoperatively.A total of 264 patients were randomized. At baseline, both groups were comparable in regards to age, sex, surgical risk, comorbidity, and analytical and nutritional parameters. The median length of the postoperative hospital stay was 5 days with no differences between the groups. A decrease in the total number of complications was observed in the immunonutrition group compared with the control group, primarily due to a significant decrease in infectious complications (23.8% vs. 10.7%, P = 0.0007). Of the infectious complications, wound infection differed significantly between the groups (16.4% vs. 5.7%, P = 0.0008). Other infectious complications were lower in the immunonutrition group but were not statistically significantly different.The implementation of ERAS protocols including immunonutrient-enriched supplements reduces the complications of patients undergoing colorectal resection.This study is registered with ClinicalTrial.gov: NCT02393976.
Odorant-Induced and Sniff-Induced Activation in the Cerebellum of the Human

Functional magnetic resonance imaging was used to test whether odorants induce activation in the cerebellum of the human. The odorants vanillin and propionic acid both induced significant activation, primarily in the posterior lateral hemispheres. Activation was concentration-dependent, greater after stimulation with higher concentration odorants. By contrast, the action of sniffing nonodorized air induced significant activation in the anterior cerebellum, primarily in the central lobule. These findings demonstrate that the cerebellum plays a role in human olfaction. A hypothesis is proposed whereby the cerebellum maintains a feedback mechanism that regulates sniff volume in relation to odor concentration.
Galaxy pairs in the Sloan Digital Sky Survey – X. Does gas content alter star formation rate enhancement in galaxy interactions?

New spectral line observations, obtained with the Jansky Very Large Array (VLA), of a sample of 34 galaxies in 17 close pairs are presented in this paper. The sample of galaxy pairs is selected to contain galaxies in close, major interactions (i.e. projected separations 3σ. We compare the H i gas fraction of the galaxies with the triggered star formation present in that galaxy. When compared to the star formation rates (SFRs) of non-pair galaxies matched in mass, redshift, and local environment, we find that the star formation enhancement is weakly positively correlated (∼2.5σ) with H i gas fraction. In order to help understand the physical mechanisms driving this weak correlation, we also present results from a small suite of binary galaxy merger simulations with varying gas fractions. The simulated galaxies indicate that larger initial gas fractions are associated with lower levels of interaction-triggered star formation (relative to an identical galaxy in isolation), but also show that high gas fraction galaxies have higher absolute SFRs prior to an interaction. We show that when interaction-driven SFR enhancements are calculated relative to a galaxy with an average gas fraction for its stellar mass, the relationship between SFR and initial gas fraction dominates over the SFR enhancements driven by the interaction. Simulated galaxy interactions that are matched in stellar mass but not in gas fraction, like our VLA sample, yield the same general positive correlation between SFR enhancement and gas fraction that we observe.
Usability of the revised NIOSH lifting equation

Following the revision of the 1981 National Institute for Occupational Safety and Health (NIOSH) lifting equation, research needs related to the new equation were outlined. Aside from epidemiological studies, the need to evaluate the usability of the 1991 NIOSH equation in realistic work environments was expressed. This paper reports on extensive experiences with training users and application of the equation in varied work settings. Qualitative results from training sessions indicated that frequency, asymmetry and duration were the parameters that required relatively longer instruction periods and resulted in the most questions. Field applications indicated that the variable nature of lifting/lowering demands found in many jobs resulted in difficulty applying the equation. Approximately 35% of 1103 lifting and lowering tasks had at least one parameter outside of acceptable ranges, while a majority of workers (62.8%) reported other manual handling tasks that are counter to assumptions made in the development of the equation. The practical implications of the findings are discussed.
Granulocyte macrophage colony‐stimulating factor enhances retinoic acid‐induced gene expression

We reported previously that treatment of human myeloblastic leukemia ML‐1 cells with all‐trans retinoic acid (ATRA) in combination with GM‐CSF enhances the granulocytic differentiation, which is induced only slightly by ATRA alone. To investigate the mechanism underlying this differentiation and the synergistic effect of ATRA and GM‐CSF, we used cDNA microarray to examine gene expression profiles of ML‐1 cells treated with ATRA and/or GM‐CSF. We identified 22 up‐regulated genes in ML‐1 cells treated with both reagents and examined the expression of these genes in cells treated with ATRA and/or GM‐CSF by Northen blot analysis. Comparison of cells treated with both reagents and cells treated with ATRA or GM‐CSF alone revealed that expression of nine of the 19 genes was induced synergistically by combined treatment with ATRA and GM‐CSF. Expression of most of these genes was increased only slightly by ATRA alone, and this induction was enhanced by the addition of GM‐CSF. These results indicate that GM‐CSF enhances ATRA‐induced gene expression. Moreover, studies with inhibitors of signaling molecules suggested that activation of JAK2 is associated with the synergistic induction of several genes by ATRA and GM‐CSF. JAK2 inhibitor suppressed induction of NBT‐reducing activity in ML‐1 cells treated with both reagents. It is likely that the enhancer effect of GM‐CSF on ATRA‐induced gene expression leads to the differentiation induced synergistically by ATRA combined with GM‐CSF. Further studies of the mechanism underlying this effect may identify better approaches for the treatment of RA‐insensitive leukemia.
Hazardous Off-Gassing of Carbon Monoxide and Oxygen Depletion during Ocean Transportation of Wood Pellets

Five ocean vessels were investigated for the characterization and quantification of gaseous compounds emitted during ocean transportation of wood pellets in closed cargo hatches from Canada to Sweden. The study was initiated after a fatal accident with several injured during discharge in Sweden. The objective with the investigation was to better understand the off-gassing and issues related to workers' exposure. Air sampling was done during transport and immediately before discharge in the undisturbed headspace air above the wood pellets and in the staircase adjacent to each hatch. The samples were analyzed with Fourier transform infrared spectroscopy and direct reading instruments. The following compounds and ranges were detected in samples from the five ships: carbon monoxide (CO) 1460–14650 ppm, carbon dioxide (CO2) 2960–21570 ppm, methane 79.9–956 ppm, butane equivalents 63–842 ppm, ethylene 2–21.2 ppm, propylene 5.3–36 ppm, ethane 0–25 ppm and aldehydes 2.3–35 ppm. The oxygen levels were between 0.8 and 16.9%. The concentrations in the staircases were almost as high as in the cargo hatches, indicating a fairly free passage of air between the two spaces. A potentially dangerous atmosphere was reached within a week from loading. The conclusions are that ocean transportation of wood pellets in confined spaces may produce an oxygen deficient atmosphere and lethal levels of CO which may leak into adjacent access spaces. The dangerous combination of extremely high levels of CO and reduced oxygen produces a fast-acting toxic combination. Measurement of CO in combination with oxygen is essential prior to entry in spaces having air communication with cargo hatches of wood pellets. Forced ventilation of staircases prior to entry is necessary. Redesign, locking and labeling of access doors and the establishment of rigorous entry procedures and training of onboard crew as well as personnel boarding ocean vessels are also important.
Naringenin-Mediated ATF3 Expression Contributes to Apoptosis in Human Colon Cancer

Naringenin (NAR) as one of the flavonoids observed in grapefruit has been reported to exhibit an anti-cancer activity. Activating transcription factor 3 (ATF3) is associated with apoptosis in human colon cancer cells. This study was performed to investigate the molecular mechanism by which NAR stimulates ATF3 expression and apoptosis in human colon cancer cells. NAR reduced the cell viability and induced an apoptosis in human colon cancer cells. ATF3 overexpression increased NAR-mediated cleaved PARP, while ATF3 knockdown attenuated the cleavage of PARP by NAR. NAR increased ATF3 expression in both protein and mRNA level, and increased the luciferase activity of ATF3 promoter in a dose-dependent manner. The responsible region for ATF3 transcriptional activation by NAR is located between −317 and −148 of ATF3 promoter. p38 inhibition blocked NAR-mediated ATF3 expression, its promoter activation and apoptosis. The results suggest that NAR induces apoptosis through p38-dependent ATF3 activation in human colon cancer cells.
Association of Sociodemographic Factors with Hope for Cure, Religiosity, and Spirituality in Patients with Venous Ulcers

OBJECTIVE: The objective of the study was to evaluate the association of sociodemographic factors with hope for cure and levels of religiosity and spirituality in patients with venous leg ulcers (VLUs). DESIGN: This was a primary, prospective, descriptive, analytical, clinical, nonrandomized study. SETTING: The study was performed at a nursing care and education center of a university hospital in interior Minas Gerais, Brazil. PATIENTS: A convenience sample of 50 adult patients with VLUs and Doppler ankle-brachial index ranging from 0.8 to 1.0 participated in the study. Patients with mixed ulcers, arterial ulcers, and diabetic foot ulcers were excluded from the study. MAIN OUTCOME MEASURES: A questionnaire assessing sociodemographic and clinical characteristics of patients, the Spirituality Self-rating Scale (SSRS), and the Herth Hope Index (HHI) were administered to all patients. MAIN RESULTS: The mean SSRS score was 10.20, and the mean HHI was 25.5, corresponding to low levels of spirituality and moderate hope for cure, respectively. Patients aged between 50 and 59 years, men, nonsmokers, and those who were unemployed had the lowest mean SSRS scores. The lowest mean HHI values were reported by patients whose ulcers had exudate and odor, those aged 20 to 39 years, retired, and living with the wound for 1 year or less. Patients who had no religion or were not practicing a religion and those who considered living with an ulcer as a punishment reported low SSRS scores. CONCLUSION: The results showed that most patients with VLUs had low levels of spirituality, did not perceive divine intervention in their daily life or practice religious activities such as prayer, and had moderate hope for cure.
Regularization of Ill-Posed Problems by Envelope Guided Conjugate Gradients

Abstract We propose a new way to iteratively solve large scale ill-posed problems by exploiting the relation between Tikhonov regularization and multiobjective optimization to obtain, iteratively, approximations to the Tikhonov L-curve and its corner. Monitoring the change of the approximate L-curves allows us to adjust the regularization parameter adaptively during a preconditioned conjugate gradient iteration, so that the desired solution can be reconstructed with a low number of iterations. We apply the technique to an idealized image reconstruction problem in positron emission tomography.
A at Single Nucleotide Polymorphism-358 Is Required for G at -420 to Confer the Highest Plasma Resistin in the General Japanese Population

Insulin resistance is a feature of type 2 diabetes. Resistin, secreted from adipocytes, causes insulin resistance in mice. We previously reported that the G/G genotype of single nucleotide polymorphism (SNP) at −420 (rs1862513) in the human resistin gene (RETN) increased susceptibility to type 2 diabetes by enhancing its promoter activity. Plasma resistin was highest in Japanese subjects with G/G genotype, followed by C/G, and C/C. In this study, we cross-sectionally analyzed plasma resistin and SNPs in the RETN region in 2,019 community-dwelling Japanese subjects. Plasma resistin was associated with SNP-638 (rs34861192), SNP-537 (rs34124816), SNP-420, SNP-358 (rs3219175), SNP+299 (rs3745367), and SNP+1263 (rs3745369) (P<10−13 in all cases). SNP-638, SNP -420, SNP-358, and SNP+157 were in the same linkage disequilibrium (LD) block. SNP-358 and SNP-638 were nearly in complete LD (r2 = 0.98), and were tightly correlated with SNP-420 (r2 = 0.50, and 0.51, respectively). The correlation between either SNP-358 (or SNP-638) or SNP-420 and plasma resistin appeared to be strong (risk alleles for high plasma resistin; A at SNP-358, r2 = 0.5224, P = 4.94×10−324; G at SNP-420, r2 = 0.2616, P = 1.71×10−133). In haplotypes determined by SNP-420 and SNP-358, the estimated frequencies for C-G, G-A, and G-G were 0.6700, 0.2005, and 0.1284, respectively, and C-A was rare (0.0011), suggesting that subjects with A at −358, generally had G at −420. This G-A haplotype conferred the highest plasma resistin (8.24 ng/ml difference/allele compared to C-G, P<0.0001). In THP-1 cells, the RETN promoter with the G-A haplotype showed the highest activity. Nuclear proteins specifically recognized one base difference at SNP-358, but not at SNP-638. Therefore, A at -358 is required for G at −420 to confer the highest plasma resistin in the general Japanese population. In Caucasians, the association between SNP-420 and plasma resistin is not strong, and A at −358 may not exist, suggesting that SNP-358 could explain this ethnic difference.
Pricing the Internet With Multibid Auctions

Usage-based or congestion-based charging schemes have been regarded as a relevant way to control congestion and to differentiate services among users in telecommunication networks; auctioning for bandwidth appears as one of several possibilities. In a previous work, the authors designed a multibid auction scheme where users compete for bandwidth at a link by submitting several couples (e.g., amount of bandwidth asked, associated unit price) so that the link allocates the bandwidth and computes the charge according to the second price principle. They showed that incentive compatibility and efficiency among other properties are verified. We propose in the present paper to extend this scheme to the case of a network by using the properties/assumptions that the backbone network is overprovisioned and the access networks have a tree structure
Googling the Brain: Discovering Hierarchical and Asymmetric Network Structures, with Applications in Neuroscience

Abstract Hierarchical organization is a common feature of many directed networks arising in nature and technology. For example, a well-defined message-passing framework based on managerial status typically exists in a business organization. However, in many real-world networks, such patterns of hierarchy are unlikely to be quite so transparent. Due to the nature in which empirical data are collated, the nodes will often be ordered so as to obscure any underlying structure. In addition, the possibility of even a small number of links violating any overall “chain of command” makes the determination of such structures extremely challenging. Here we address the issue of how to reorder a directed network to reveal this type of hierarchy. In doing so, we also look at the task of quantifying the level of hierarchy, given a particular node ordering. We look at a variety of approaches. Using ideas from the graph Laplacian literature, we show that a relevant discrete optimization problem leads to a natural hierarchical node ranking. We also show that this ranking arises via a maximum likelihood problem associated with a new range-dependent hierarchical random-graph model. This random-graph insight allows us to compute a likelihood ratio that quantifies the overall tendency for a given network to be hierarchical. We also develop a generalization of this node-ordering algorithm based on the combinatorics of directed walks. In passing, we note that Google's PageRank algorithm tackles a closely related problem, and may also be motivated from a combinatoric, walk-counting viewpoint. We illustrate the performance of the resulting algorithms on synthetic network data, and on a real-world network from neuroscience where results may be validated biologically.
Mammalian Evolution May not Be Strictly Bifurcating

The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide-long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1–4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100–80 Ma and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. Given the timing of tectonics, of placental mammalian divergences, and the fossil record, a Laurasian rather than Gondwanan origin of placental mammals seems the most parsimonious explanation.