Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation

A trait's genomic architecture can affect the rate and mechanism of adaptation, and although many ecologically-important traits are polygenic, most studies connecting genotype, phenotype, and fitness in natural populations have focused on traits with relatively simple genetic bases. To understand the genetic basis of polygenic adaptation, we must integrate genomics, phenotypic data, ecology, and fitness effects for a genetically tractable, polygenic trait; snake venoms provide such a system for studying polygenic adaptation because of their genetic tractability and vital ecological role in feeding and defense. We used a venom transcriptome-proteome map, quantitative proteomics, genomics, and fitness assays in sympatric prey to construct a genotype-phenotype-fitness map for the venoms of an island-mainland pair of rattlesnake populations. Reciprocal fitness experiments demonstrated that each population was locally adapted to sympatric prey. We identified significant expression differentiation with little to no coding-sequence variation across populations, demonstrating that expression differentiation was exclusively the genetic basis of polygenic adaptation. Previous research on the genetics of adaptation, however, has largely been biased toward investigating protein-coding regions because of the complexity of gene regulation. Our results showed that biases at the molecular level can be in the opposite direction, highlighting the need for more systematic comparisons of different molecular mechanisms underlying rapid, adaptive evolution in polygenic traits.
Effect of pH on the development of acrosomal responsiveness of human sperm

Human sperm incubated in vitro gradually become responsive to inducers of the acrosome reaction. The roles of constituents of the incubation medium are not well understood. These experiments tested the effect of the extracellular pH on sperm acrosomal responsiveness. Sperm were incubated 24 h in media with pH varying between 6.7 and 7.6 and then exposed to progesterone to determine the number of sperm that had become acrosomally responsive. The number of responsive sperm was very low following incubation at pH 6.7–7.0, and increased with the pH over the range 7.0–7.6. Sperm incubated at low pH were not damaged as assessed by motility or viability, and if they were transferred to medium of high pH for 8 h, the inhibition of acrosomal responsiveness was reversed. Inhibition of acrosomal responsiveness at low pH was not due to impaired loss of sperm cholesterol, but was correlated with a reduced intracellular pH. The inhibition of acrosomal responsiveness by media of low pH may result from preventing the normal capacitation‐related rise in intracellular pH.
Resource allocation for multipoint-to-multipoint orthogonal multicarrier division duplexing

Orthogonal multicarrier division duplexing (MDD) is a new duplexing scheme that gains the advantages of both time division duplexing and frequency division duplexing. Resource allocation for multipoint-to-multipoint (M2M) MDD is considered in this paper. We propose joint subcarrier and power allocation for M2M MDD that maximizes the sum rate of the network under either total or individual power constraint. Simulation results show that MDD outperforms conventional TDD and TDD-OFDMA systems. Some insights on M2M MDD under different channel conditions are given and convergence of the proposed algorithm is shown through simulation results.
Frameless robotically targeted stereotactic brain biopsy: feasibility, diagnostic yield, and safety.

OBJECT Frameless stereotactic brain biopsy has become an established procedure in many neurosurgical centers worldwide. Robotic modifications of image-guided frameless stereotaxy hold promise for making these procedures safer, more effective, and more efficient. The authors hypothesized that robotic brain biopsy is a safe, accurate procedure, with a high diagnostic yield and a safety profile comparable to other stereotactic biopsy methods. METHODS This retrospective study included 41 patients undergoing frameless stereotactic brain biopsy of lesions (mean size 2.9 cm) for diagnostic purposes. All patients underwent image-guided, robotic biopsy in which the SurgiScope system was used in conjunction with scalp fiducial markers and a preoperatively selected target and trajectory. Forty-five procedures, with 50 supratentorial targets selected, were performed. RESULTS The mean operative time was 44.6 minutes for the robotic biopsy procedures. This decreased over the second half of the study by 37%, from 54.7 to 34.5 minutes (p < 0.025). The diagnostic yield was 97.8% per procedure, with a second procedure being diagnostic in the single nondiagnostic case. Complications included one transient worsening of a preexisting deficit (2%) and another deficit that was permanent (2%). There were no infections. CONCLUSIONS Robotic biopsy involving a preselected target and trajectory is safe, accurate, efficient, and comparable to other procedures employing either frame-based stereotaxy or frameless, nonrobotic stereotaxy. It permits biopsy in all patients, including those with small target lesions. Robotic biopsy planning facilitates careful preoperative study and optimization of needle trajectory to avoid sulcal vessels, bridging veins, and ventricular penetration.
Automatic Analysis of Author Judgment in Scientific Articles Based on Semantic Annotation

In this paper we describe how the annotation methodology adopted in our approach allows us to explain the organization of indexed references in scientific research articles. We identify the semantic values of author judgments in the text segments containing indexed references. We use an automated semantic annotation platform to annotate our corpora. Exploiting this result, we obtain a representation of the annotation distribution on different scales. Finally, we present two evaluations of the annotation.
IntelliCages and automated assessment of learning in group-housed mice

IntelliCage is a fully automated, computer controlled system, which can be used for long-term monitoring of behavior of group-housed mice. Using standardized experimental protocols we can assess cognitive abilities and behavioral flexibility in appetitively and aversively motivated tasks, as well as measure social influences on learning of the subjects. We have also identified groups of neurons specifically activated by appetitively and aversively motivated learning within the amygdala, function of which we are going to investigate optogenetically in the future.
International Journal of High Performance Computing Applications towards an Accurate Model for Collective Communications towards an Accurate Model for Collective Communications

The performance of the MPI's collective communications is critical in most MPI-based applications. A general algorithm for a given collective communication operation may not give good performance on all systems due to the differences in architectures, network parameters and the storage capacity of the underlying MPI implementation. Hence, collective communications have to be tuned for the system on which they will be executed. In order to determine the optimum parameters of collective communications on a given system in a time-efficient manner, the collective communications need to be modeled efficiently. In this paper, we discuss various techniques for modeling collective communications.
An Unconventional Human Ccr4-Caf1 Deadenylase Complex in Nuclear Cajal Bodies

ABSTRACT mRNA deadenylation is a key process in the regulation of translation and mRNA turnover. In Saccharomyces cerevisiae, deadenylation is primarily carried out by the Ccr4p and Caf1p/Pop2p subunits of the Ccr4-Not complex, which is conserved in eukaryotes including humans. Here we have identified an unconventional human Ccr4-Caf1 complex containing hCcr4d and hCaf1z, distant human homologs of yeast Ccr4p and Caf1p/Pop2p, respectively. The hCcr4d-hCaf1z complex differs from conventional Ccr4-Not deadenylase complexes, because (i) hCaf1z and hCcr4d concentrate in nuclear Cajal bodies and shuttle between the nucleus and cytoplasm and (ii) the hCaf1z subunit, in addition to rapid deadenylation, subjects substrate RNAs to slow exonucleolytic degradation from the 3′ end in vitro. Exogenously expressed hCaf1z shows both of those activities on reporter mRNAs in human HeLa cells and stimulates general mRNA decay when restricted to the cytoplasm by deletion of its nuclear localization signal. These observations suggest that the hCcr4d-hCaf1z complex may function either in the nucleus or in the cytoplasm after its nuclear export, to degrade polyadenylated RNAs, such as mRNAs, pre-mRNAs, or those RNAs that are polyadenylated prior to their degradation in the nucleus.
Restorative Treatment Thresholds: Factors Influencing the Treatment Thresholds and Modalities of General Dentists in Kuwait

Objectives: This study investigated the thresholds at which general dentists in Kuwait would restore approximal and occlusal carious lesions and examined the demographic characteristics of the dentists in relation to their decision making. Subjects and Methods: The study population consisted of a random sample of 185 general dentists practicing in the Ministry of Health of Kuwait. A survey questionnaire was administered. The questionnaire presented different stages and locations of carious lesions; the participants were asked to identify the stage at which a restoration is required under different conditions, the preparation technique, and their choice of restorative material. Results: For approximal carious lesions, 74 (40%) of the participants reported that they would restoratively intervene when the carious lesion reached the outer third of the dentin. A total of 91 (49.2%) reported the use of traditional class II restorations. For occlusal carious lesions, 128 (69.2%) said they would intervene when lesions reached the middle third of the dentin. 146 (78.9%) said they would remove the carious tissue only in their preparation. For both approximal and occlusal lesions, the participants preferred resin composite as the material for restoration. Conclusions: The respondents tended to delay restorative intervention until dentinal penetration of the caries. Resin restorative materials were used in conservatively prepared cavities. Participants chose a conservative approach for occlusal lesions but still believed in a traditional approach when it concerned approximal lesions. Experience, university dental education, and participation in continuous education courses were most significantly related to restorative treatment.
The Changing Locus of Health Data Production and Use: Patient-Generated Health Data, Observations of Daily Living, and Personal Health Information Management

Despite the growing attention of researcher, healthcare managers and policy makers, data gathering and information management practices are largely untheorized areas. In this work are presented and discussed some early-stage conceptualizations: Patient-Generated Health Data (PGHD), Observations of Daily Living (ODLs) and Personal Health Information Management (PHIM). As I shall try to demonstrate, these labels are not neutral rather they underpin quite different perspectives with respect to health, patient-doctor relationship, and the status of data.
Institutional Entrepreneurship, Partaking, and Convening

This paper proposes that processes of institutional change vary depending on the form taken by the three factors that define them: agency, resource mobilization, and opportunity. The paper builds on a conceptualization of agency that considers that change may result from diverse forms of agency (i.e. strategic, routine, and sense-making). It develops the concept of resource mobilization, focusing on the process as opposed to the skills required for mobilization. It then suggests that the mobilization of resources, support and acceptance, accompanying the diffusion and legitimation of institutional changes may follow leverage, partaking, or convening processes. Finally, the paper defines institutional opportunity as an objective condition of organizational fields, suggesting that fields may be opportunity opaque, transparent, or hazy. Opportunities, of course, only become real when perceived by actors. Building on current sociological work, the paper suggests that actors’ perception of the opportunity transparency of fields varies with their temporal orientation and social networks. Considering the possible variations of agency, resource mobilization, and opportunity, and how they may combine, the paper defines three profiles of institutional change: entrepreneurship, partaking, and convening.
Word Learning in the Wild: What Natural Data Can Tell Us

When a child first begins to acquire a lexicon, the sources of word-meanings must be available from the situational context. However, it has been argued that the situational availability of the meanings of relational terms, such as verbs, is lower than that of whole-object labels, such as nouns. In this paper, we present a corpus of child-directed language, paired with situational descriptions, that enables us to explore the situational availability of word-meanings using a computational learner.
Extending sense-making models with ideas from cognition and learning theories

In this paper we extend existing sense-making models by adding detail on types of conceptual change and cognitive mechanisms taken from theories of cognition and learning. Our extended model aims to offer a more complete picture of the cognitive processes of sense-making, including the underlying cognitive mechanisms and different types of conceptual changes so that we can link observations to theory. We conducted a preliminary test of the model against think-aloud protocols of users performing intelligence analysis tasks using a multilingual, multimedia information system. Their sense-making processes were consistent with our iterative model of search and sense-making loops. Most of the cognitive mechanisms derived from the literature appeared, with a prevalence of data-driven mechanisms.
Discovery of Selective Irreversible Inhibitors for Bruton’s Tyrosine Kinase

The importance of B cells in rheumatoid arthritis (RA) pathogenesis has been recently demonstrated in several clinical studies using the anti-CD20 antibody rituximab, which selectively depletes B cells. A recent phase III clinical trial led to the FDA approval of rituximab for a subset of RA patients. Bruton’s tyrosine kinase (Btk), a member of Tec family kinases, is a key component in the B-cell receptor signal pathway (BCR). Upon activation by upstream kinases (for example, Lyn and Syk), Btk phosphorylates and thereby activates phospholipase-Cg (PLCg), leading to several important downstream events including calcium ion transportation, NF-kB activation, and (auto)antibody generation. Previous biological studies (genetic loss of function and siRNA knockdown) strongly suggest that Btk is also a mediator of proinflammatory signals. Taken together, these studies indicate Btk may be a potential target for the treatment of RA. However, despite the previous discovery of LFM-A13 as a selective Btk inhibitor, there is no published study that has demonstrated that inhibition of Btk activity leads to in vivo efficacy in an animal model of rheumatoid arthritis. As ATP binding sites in kinases are highly conserved, it is a formidable task to develop selective ATP competitive kinase inhibitors. Among several approaches, the use of electrophilic inhibitors has been shown as a viable method to achieve selectivity. Considering the relative scarcity of knowledge on “chemical knockdown” of Btk activity, it is crucial to discover a potent and selective tool compound for this kinase. Herein, we describe the discovery of a selective, irreversible Btk inhibitor and its efficacy in a mouse RA model. An initial campaign to scan for scaffolds capable of inhibiting Btk’s kinase activity identified compound 1 as having
Assessing rationales for inclusiveness in meta-analytic samples

The desirability of including all relevant studies in a meta-analysis has been defended by at least six arguments: (1) Any inclusion/exclusion criteria would inevitably reflect unique biases of the individual meta-analyst; (2) The global methodological quality of studies cannot be reliably assessed; (3) There is evidence to suggest that effect size and methodological quality do not covary; (4) Flaws in the inclusive sample are likely to be distributed unsystematically; (5) Inclusiveness combined with describing the characteristics of the individual studies allows the meta-analyst to determine the effect that any number of moderating variables has on overall effect size estimates; and (6) A number of studies with nonsignificant findings cannot be retrieved, and further inclusion/exclusion criteria would exacerbate the “file drawer” problem. Each of these six rationales will be reconsidered. Results indicate that these rationales receive little empirical support, and thus deserve to be empirically assessed .
Impact evaluation of physical length of shared risk link groups on optical network availability using Monte Carlo simulation

In optical networks a group of logically distinct links can unintentionally share a physical resource (e.g, a cable or a duct). Such a group, called shared risk link group (SRLG), introduces a situation where a single failure of common resource can cause multiple failures. Failure of common resource usually occurs due to physical force (e.g, digging or earthquake) and causes failures of multiple links. Specifically, such a failure can cause both working and spare wavelength path of a logical connection between two edge nodes to fail at the same time, leaving them disconnected until a repair is done. The usual approach to solving this problem consists of introducing more spare capacity to the network and also using a routing algorithm that takes SRLGs into account when computing paths. Such a routing algorithm avoids creating working and spare path pairs that have links contained in the same SRLG, to minimize the negative impact of SRLG failure on logical connection availability. In this paper the impact of physical length of the SRLGs on network availability is evaluated using Monte Carlo simulation. New simulation model for availability evaluation is implemented by discrete-event network simulator ns-3. Implementation approach is discussed, and an overview of model features is provided. For simple cases, Monte Carlo simulation results obtained by using the model are compared to analytical results. The availability results for the general case are obtained using Monte Carlo simulation and discussed.
Model-Based Checkpoint Scheduling for Volatile Resource Environments

In this paper, we describe a system for application checkpoint scheduling in volatile resource environments. Our approach combines historical measurements of resource availability with an estimate of checkpoint/recovery delay to generate checkpoint intervals that minimize overhead. When executing in a desktop computing or resource harvesting context, long-running applications must checkpoint, since resources can be reclaimed by their owners without warning. Our system records the historical availability from each resource and fits a statistical model to the observations using either Maximum Likelihood Estimation (MLE) or Expectation Maximization (EM). When an application is initiated on a particular resource, the system uses the computed distribution to parameterize a Markov state-transition model for the application’s execution, evaluates the expected overhead as a function of the checkpoint interval, and numerically optimizes this quantity. Using Condor as a target platform, we investigate the effectiveness of this technique fitting exponential, Weibull, 2phase hyperexponential and 3-phase hyperexponential distributions to observed availability data. To verify our method and compare the distributions each against the same conditions, we use observations taken from the Condor pool at the University of Wisconsin and trace-based simulation. We examine the practical value of our approach by observing an implementation of our system when applied to a test application that is then run on the “live” Condor system. Finally, we conclude with a verification of the simulated results against the experimental observations. Our results indicate that application efficiency is relatively insensitive to This work was supported by National Science Foundation Grants numbered NGS-0305390 and CCR-0331654. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Copyright 200X ACM X-XXXXX-XX-X/XX/XX . $5.00. the choice of distribution (among the ones we investigate) but that induced network load is not.
Interspersed Meaningful Learning Questions as Semantic Cues for Poor Comprehenders.

GOOD AND POOR COMPREHENDERS (fifth grade children, N = 93) read an 800-word passage and after every 2 paragraphs received either a meaningful learning question requiring the organization of facts under given concepts, a rote learning question requiring literal recall of passage information, or no adjunct question of any kind. For most measures of text recall, good comprehenders recalled more than the poor comprehenders; and the type of treatment presented did not have a significant (p > .05) effect. For poor comprehenders, however, meaningful learning post questions yielded significantly (p < .05) greater recall of facts from the question-related paragraphs than did rote learning post questions or no questions of any type. On the measure of recall of subordinate material, the performance of the poor comprehenders given meaningful learning post questions did not differ significantly from that of the good comprehenders, regardless of the kind of treatment the latter received.
Nearest neighbor queries

A frequently encountered type of query in Geographic Information Systems is to find the k nearest neighbor objects to a given point in space. Processing such queries requires substantially different search algorithms than those for location or range queries. In this paper we present an efficient branch-and-bound R-tree traversal algorithm to find the nearest neighbor object to a point, and then generalize it to finding the k nearest neighbors. We also discuss metrics for an optimistic and a pessimistic search ordering strategy as well as for pruning. Finally, we present the results of several experiments obtained using the implementation of our algorithm and examine the behavior of the metrics and the scalability of the algorithm.