Miracle-dz/UniFAR-FTUs huggingface dataset:
Logarithmic distributions prove that intrinsic learning is Hebbian [version 2; peer review: 2 approved]

In this paper, we present data for the lognormal distributions of spike rates, synaptic weights and intrinsic excitability (gain) for neurons in various brain areas, such as auditory or visual cortex, hippocampus, cerebellum, striatum, midbrain nuclei. We find a remarkable consistency of heavy-tailed, specifically lognormal, distributions for rates, weights and gains in all brain areas examined. The difference between strongly recurrent and feed-forward connectivity (cortex vs. striatum and cerebellum), neurotransmitter (GABA (striatum) or glutamate (cortex)) or the level of activation (low in cortex, high in Purkinje cells and midbrain nuclei) turns out to be irrelevant for this feature. Logarithmic scale distribution of weights and gains appears to be a general, functional property in all cases analyzed. We then created a generic neural model to investigate adaptive learning rules that create and maintain lognormal distributions. We conclusively demonstrate that not only weights, but also intrinsic gains, need to have strong Hebbian learning in order to produce and maintain the experimentally attested distributions. This provides a solution to the long-standing question about the type of plasticity exhibited by intrinsic excitability.
Clinical significance of primary symptoms in women with placental abruption

Abstract Background: To evaluate the clinical significance of primary symptoms in women with placental abruption. Methods: A retrospective study of 273 cases of placental abruption was performed. The subjects were classified into two groups according to primary symptoms: 210 cases of the vaginal bleeding group and 63 cases of the abdominal pain group. The clinical features, maternal and neonatal outcomes were compared between two groups. Results: The incidence of preeclampsia and preterm birth in the vaginal bleeding group was significantly lower than abdominal pain group, while the incidence of premature rupture of membrane (PROM) in the former group was higher than that in the latter group. Both fetal and maternal outcomes were significantly poorer in the abdominal pain group than in the vaginal bleeding group in terms of rate of abnormal fetal heart monitoring (FHR), concealed abruption, abruption area over 50%, uteroplacental apoplexy, volume of postpartum hemorrhage, rate of blood transfusion, neonatal asphyxia and acidemia. Conclusions: Primary symptoms of placental abruption were associated with preterm birth, preeclampsia and PROM, which could predict pregnancy outcomes effectively.
The BioGRID interaction database: 2015 update

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.
Manipulation among the arbiters of collective intelligence: how wikipedia administrators mold public opinion

Our reliance on networked, collectively built information is a vulnerability when the quality or reliability of this information is poor. Wikipedia, one such collectively built information source, is often our first stop for information on all kinds of topics; its quality has stood up to many tests, and it prides itself on having a "Neutral Point of View". Enforcement of neutrality is in the hands of comparatively few, powerful administrators. We find a surprisingly large number of editors who change their behavior and begin focusing more on a particular controversial topic once they are promoted to administrator status. The conscious and unconscious biases of these few, but powerful, administrators may be shaping the information on many of the most sensitive topics on Wikipedia; some may even be explicitly infiltrating the ranks of administrators in order to promote their own points of view. Neither prior history nor vote counts during an administrator's election can identify those editors most likely to change their behavior in this suspicious manner. We find that an alternative measure, which gives more weight to influential voters, can successfully reject these suspicious candidates. This has important implications for how we harness collective intelligence: even if wisdom exists in a collective opinion (like a vote), that signal can be lost unless we carefully distinguish the true expert voter from the noisy or manipulative voter.
Supporting Multi-dimensional Range Query in HD Tree

There are two basic concerns for supporting multi-dimensional range query in P2P overlay networks. The first is to preserve data locality in the process of data space partitioning, and the second is the maintenance of data locality among data items with an exponentially expanding rate and an exponentially extending rate. The first problem has been well addressed by using recursive decomposition schemes, such as Quad tree, K-d tree, Z-order, and Hilbert curve. While the second problem was recently identified by our novel data structure: HD Tree. This paper is a follow-up to our previous work in HD Tree. In this paper, we explore how data locality can be easily maintained, and how range query can be efficiently supported in HD Tree. This is done by introducing two basic routing strategies, hierarchical routing and distributed routing. Although hierarchical routing can be applied to any two nodes in the system, it generates high volume traffic towards nodes near the root, and has very limited options to cope with a node failure. On the other hand, distributed routing concerns source and destination pairs only at the same depth, but traffic load is bound to some nodes at two neighboring depths, and multiple options can be found to redirect a routing request. Because HD Tree supports multiple routes between any two nodes in the system, routing in HD Tree is very flexible, and can be designed for many purposes, like fault tolerance, or dynamic load balancing. Distributed Routing Oriented Combined Routing algorithm is one such routing strategies implemented so far. It is a hybrid algorithm combining advantages from both the hierarchical routing and the distributed routing. The experimental results show that the DROCR algorithm achieves considerable performance gain over the equivalent tree routing at the highest depth examined. In the experiment of supporting multi-dimensional range query, we employ the Z-order space filling curve over the HD Tree overlay layer. We are expecting that the performance of range query will vary proportionally with the change of range size, and reasonably with the increase of dimensionality.
Computing Marginals Using MapReduce: Keynote talk paper

We consider the problem of computing the data-cube marginals of a fixed order k (i.e., all marginals that aggregate over k dimensions), using a single round of MapReduce. The focus is on the relationship between the reducer size (number of inputs allowed at a single reducer) and the replication rate (number of reducers to which an input is sent). We show that the replication rate is minimized when the reducers receive all the inputs necessary to compute one marginal of higher order. That observation lets us view the problem as one of covering sets of k dimensions with sets of a larger size m, a problem that has been studied under the name "covering numbers. " We offer a number of constructions that, for different values of k and m meet or come close to yielding the minimum possible replication rate for a given reducer size.
Early-Life Family Structure and Microbially Induced Cancer Risk

Background Cancer may follow exposure to an environmental agent after many decades. The bacterium Helicobacter pylori, known to be acquired early in life, increases risk for gastric adenocarcinoma, but other factors are also important. In this study, we considered whether early-life family structure affects the risk of later developing gastric cancer among H. pylori + men. Methods and Findings We examined a long-term cohort of Japanese-American men followed for 28 y, and performed a nested case-control study among those carrying H. pylori or the subset carrying the most virulent cagA+ H. pylori strains to address whether family structure predicted cancer development. We found that among the men who were H. pylori+ and/or cagA + (it is possible to be cagA+ and H. pylori − if the H. pylori test is falsely negative), belonging to a large sibship or higher birth order was associated with a significantly increased risk of developing gastric adenocarcinoma late in life. For those with cagA+ strains, the risk of developing gastric cancer was more than twice as high (odds ratio 2.2; 95% confidence interval 1.2–4.0) among those in a sibship of seven or more individuals than in a sibship of between one and three persons. Conclusions These results provide evidence that early-life social environment plays a significant role in risk of microbially induced malignancies expressing five to eight decades later, and these findings lead to new models to explain these interactions.
Assessing the probability of rare climate events

This article focuses on the use of Bayesian methods in assessing the probability of rare climate events, and more specifically the potential collapse of the meridional overturning circulation (MOC) in the Atlantic Ocean. It first provides an overview of climate models and their use to perform climate simulations, drawing attention to uncertainty in climate simulators and the role of data in climate prediction, before describing an experiment that simulates the evolution of the MOC through the twenty-first century. MOC collapse is predicted by the GENIE-1 (Grid Enabled Integrated Earth system model) for some values of the model inputs, and Bayesian emulation is used for collapse probability analysis. Data comprising a sparse time series of five measurements of the MOC from 1957 to 2004 are analysed. The results demonstrate the utility of Bayesian analysis in dealing with uncertainty in complex models, and in particular in quantifying the risk of extreme outcomes.
Stabilisation of infinitesimally rigid formations of multi-robot networks

This article considers the design of a formation control for multivehicle systems that uses only local information. The control is derived from a potential function based on an undirected infinitesimally rigid graph that specifies the target formation. A potential function is obtained from the graph, from which a gradient control is derived. Under this controller the target formation becomes a manifold of equilibria for the multivehicle system. It is shown that infinitesimal rigidity is a sufficient condition for local asymptotical stability of the equilibrium manifold. A complete study of the stability of the regular polygon formation is presented and results for directed graphs are presented as well. Finally, the controller is validated experimentally.
The apnea test for brain death determination: an alternative approach.

INTRODUCTION Problems associated with the standard apnea test relate to overshooting or undershooting the target PaCO2, potentially compromising the viability of organs for transplantation or invalidating the test. MATERIALS AND METHODS In 60 adult patients, the authors used an alternative method using exogenously administered CO2 and measurement of end-tidal CO2. RESULTS All patients achieved an adequate respiratory stimulus (mean increase in PaCO2 was 28+/-3 mmHg, postapnea test pH was 7.20+/-.02). There was a clinically insignificant reduction in arterial blood pressure during testing, but no other complications occurred. Multiple regression analysis demonstrated a correlation between the predicted PaCO2 (predicted from the end-tidal CO2) and measured PaCO2 (64+/-9 versus 67+/-9; r=.75169, p<0.0001). CONCLUSION Exogenously administered CO2 as an alternative method for the standard apnea test was a reliable and safe method, with minimal complications that offers several advantages over the standard method.
Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde–hydrazine chemistry and protease-cleavable linkers

The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde–hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. This initiator nucleotide was efficiently incorporated into RNA, and the modified RNAs were quantitatively coupled to a peptide derivative displaying a hydrazine moiety at one end, a biotin tag at the other, and a trypsin-cleavable sequence in between. RNA conjugates could be easily isolated by affinity chromatography on streptavidin agarose and quantitatively cleaved off the support by trypsin treatment without detectable RNA degradation. The strategy described here may allow the incorporation of various new features into enzymatically synthesized RNA under mild conditions.
Unified algebraic theory of sorting, routing, multicasting, and concentration networks

Multistage interconnection networks (MINs) are commonly deployed in sorting, switching, and other applications. Arithmetic over MINs for various applications is hereby unified in algebra. The key is to structure the signal alphabet as a distributive lattice instead of an ordered set. The theoretic unification enhances the mathematical understanding of properties of MINs and, in particular, demystifies various 0-1 principles. Conventional applications of MINs are all for point-to-point transmissions, while the unified theory applies to multicasting as well. The Multicast Concentrator Theorem is generalized into the Boolean Concentrator Theorem, which is useful in recursive construction of multicast switches with the feature of priority treatment. Meanwhile, the concomitant theory of cut-through coding is introduced for delay-free signal propagation through a MIN.
Return to sport following anterior cruciate ligament reconstruction surgery: a systematic review and meta-analysis of the state of play

Background An athlete's intention to return to sport following anterior cruciate ligament (ACL) injury is a major indication for surgical intervention. Purpose The purpose of this review was to determine postoperative return-to-sport outcomes after ACL reconstruction surgery. Study design Meta-analysis and systematic review Methods Electronic databases including Medline, Embase, SPORTDiscus and CINAHL were searched from the earliest possible entry to April 2010. Studies were included that reported the number of patients returning to sports participation following ACL reconstruction surgery. The results were presented using the World Health Organization's International Classification of Functioning, Disability and Health as a framework and combined using proportion meta-analyses. Results Forty-eight studies evaluating 5770 participants at a mean follow-up of 41.5 months were included for review. Overall, 82% of participants had returned to some kind of sports participation, 63% had returned to their preinjury level of participation, and 44% had returned to competitive sport at final follow-up. Approximately 90% of participants achieved normal or nearly normal knee function when assessed postoperatively using impairment-based outcomes such as laxity and strength, and 85% when using activity-based outcomes such as the International Knee Documentation Committee knee evaluation form. Fear of reinjury was the most common reason cited for a postoperative reduction in or cessation of sports participation. Conclusion The relatively low rate of return to competitive sport despite the high rates of successful outcome in terms of knee impairment-based function suggests that other factors such as psychological factors may be contributing to return-to-sport outcomes.
Possible chromosomal and germline integration of human herpesvirus 7

Human herpesvirus 7 (HHV-7) is a betaherpesvirus, and is phylogenetically related to both HHV-6A and HHV-6B. The presence of telomeric repeat sequences at both ends of its genome should make it equally likely to integrate into the human telomere as HHV-6. However, numerous studies have failed to detect germline integration of HHV-7, suggesting an important difference between the HHV-6A/-6B and HHV-7 genomes. In search of possible germline integrated HHV-7, we developed a sensitive and quantitative real-time PCR assay and discovered that primers designed against some parts of the HHV-7 genome can frequently miss HHV-7 positive clinical samples even though they work efficiently in cell-culture-derived HHV-7 positive materials. Using a primer pair against the U90 ORF of HHV-7, we identified a possible case of germline integration of HHV-7 with one copy of viral genome per cell in both peripheral blood cells and hair follicles. Chromosomal integration of HHV-7 in these individuals was confirmed by fluorescence in situ hybridization analysis. Germline integration of HHV-7 was further confirmed by detection of ~2.6 copies of HHV-7 in the hair follicles of one of the parents. Our results shed light on the complex nature of the HHV-7 genome in human-derived materials in comparison to cell-culture-derived materials and show the need for stringent criteria in the selection of primers for epidemiological HHV-7 studies.
Polynomial-Time Approximation Algorithms for the Ising Model

This paper is concerned with computational solutions to some classical combinatorial problems in statistical physics. These problems stem from the Ising model, which has been the focus of much attention in the physics and mathematics communities since it was first introduced by Lenz [14] and Ising [7] in the early 1920s. We will not present a detailed historical account here: a very readable survey is given by Cipra [2], while Welsh [18] sets the Ising model in the context of other combinatorial problems in statistical physics.
Improving Evolutionary Testing By Flag Removal

This paper argues that Evolutionary testing can be improved by transforming programs with flags into flag free programs. The approach is evaluated by comparing results from the application of the Daimler-Chrysler Evolutionary Testing System to programs with flags and their transformed flag-free counterparts. The results of this empirical study are very encouraging. Programs which could not be fully covered become fully coverable and the number of generations required to achieve full coverage is greatly reduced.
Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues

An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements. In this work, a systematic attempt is made to tackle this issue for the conventional myosin. By judiciously combining a range of computational techniques with different approximations and strength, which include targeted molecular dynamics, normal mode analysis, and statistical coupling analysis, we are able to identify a set of important residues and propose their relevant function during the recovery stroke of myosin. These analyses also allowed us to make connections with previous experimental and computational studies in a critical manner. The behavior of the widely used reporter residue, Trp501, in the simulations confirms the concern that its fluorescence does not simply reflect the relay loop conformation or active-site open/close but depends subtly on its microenvironment. The findings in the targeted molecular dynamics and a previous minimum energy path analysis of the recovery stroke have been compared and analyzed, which emphasized the difference and complementarity of the two approaches. In conjunction with our previous studies, the current set of investigations suggest that the modulation of structural flexibility at both the local (e.g., active-site) and domain scales with strategically placed “hotspot” residues and phosphate chemistry is likely the general feature for mechanochemical coupling in many molecular motors. The fundamental strategies of examining both collective and local changes and combining physically motivated methods and informatics-driven techniques are expected to be valuable to the study of other molecular motors and allosteric systems in general.
EHPnet: Growing Up Healthy

Relapse after completing adjuvant tamoxifen therapy is a persistent threat for women with hormoneresponsive breast cancer. Third-generation aromatase inhibitors, such as letrozole, provide a new option for extended adjuvant hormonal therapy after 5 years of tamoxifen. MA.17 was conducted to determine whether letrozole improves outcome after discontinuation of tamoxifen. Postmenopausal women with hormone receptor-positive breast cancer (N = 5,187) were randomized to letrozole 2.5 mg or placebo once daily for 5 years. At a median follow-up of 30 months, letrozole significantly improved disease-free survival (DFS; P \ 0.001), the primary end point, compared with placebo (hazard ratio [HR] for recurrence or contralateral breast cancer 0.58; 95% confidence interval [CI] 0.45, 0.76] P \ 0.001). Furthermore, letrozole significantly improved distant DFS (HR = 0.60; 95% CI 0.43, 0.84; P = 0.002) and, in women with node-positive tumors, overall survival (HR = 0.61; 95% CI 0.38, 0.98; P = 0.04). Clinical benefits, including an overall survival advantage, were also seen in women who crossed over from placebo to letrozole after unblinding, indicating that tumors remain sensitive to hormone therapy despite a prolonged period since discontinuation of tamoxifen. The efficacy and safety of letrozole therapy beyond 5 years is being assessed in a re-randomization study, following the emergence of new data suggesting that clinical benefit correlates with the duration of letrozole. MA.17 showed that letrozole is extremely well-tolerated relative to placebo. Letrozole should be considered for all women completing tamoxifen; new results from the postunblinding analysis suggest that letrozole treatment should also be considered for all disease-free women for periods up to 5 years following completion of adjuvant tamoxifen.