Miracle-dz/UniFAR-FTUs huggingface dataset:
The yeast protein kinase Mps1p is required for assembly of the integral spindle pole body component Spc42p

Saccharomyces cerevisiae MPS1 encodes an essential protein kinase that has roles in spindle pole body (SPB) duplication and the spindle checkpoint. Previously characterized MPS1 mutants fail in both functions, leading to aberrant DNA segregation with lethal consequences. Here, we report the identification of a unique conditional allele, mps1–8, that is defective in SPB duplication but not the spindle checkpoint. The mutations in mps1-8 are in the noncatalytic region of MPS1, and analysis of the mutant protein indicates that Mps1-8p has wild-type kinase activity in vitro. A screen for dosage suppressors of the mps1-8 conditional growth phenotype identified the gene encoding the integral SPB component SPC42. Additional analysis revealed that mps1-8 exhibits synthetic growth defects when combined with certain mutant alleles of SPC42. An epitope-tagged version of Mps1p (Mps1p-myc) localizes to SPBs and kinetochores by immunofluorescence microscopy and immuno-EM analysis. This is consistent with the physical interaction we detect between Mps1p and Spc42p by coimmunoprecipitation. Spc42p is a substrate for Mps1p phosphorylation in vitro, and Spc42p phosphorylation is dependent on Mps1p in vivo. Finally, Spc42p assembly is abnormal in a mps1-1 mutant strain. We conclude that Mps1p regulates assembly of the integral SPB component Spc42p during SPB duplication.
Improved Practical Matrix Sketching with Guarantees

Matrices have become essential data representations for many large-scale problems in data analytics, and hence matrix sketching is a critical task. Although much research has focused on improving the error/size tradeoff under various sketching paradigms, the many forms of error bounds make these approaches hard to compare in theory and in practice. This paper attempts to categorize and compare the most known methods under row-wise streaming updates with provable guarantees, and then to tweak some of these methods to gain practical improvements while retaining guarantees. For instance, we observe that a simple heuristic iSVD, with no guarantees, tends to outperform all known approaches in terms of size/error trade-off. We modify the best performing method with guarantees, FREQUENTDIRECTIONS, under the size/error trade-off to match the performance of iSVD and retain its guarantees. We also demonstrate some adversarial datasets where iSVD performs quite poorly. In comparing techniques in the time/error trade-off, techniques based on hashing or sampling tend to perform better. In this setting, we modify the most studied sampling regime to retain error guarantee but obtain dramatic improvements in the time/error trade-off. Finally, we provide easy replication of our studies on APT, a new testbed which makes available not only code and datasets, but also a computing platform with fixed environmental settings.
High-Dimensional Clustering with Sparse Gaussian Mixture Models

We consider the problem of clustering high-dimensional data using Gaussian Mixture Models (GMMs) with unknown covariances. In this context, the ExpectationMaximization algorithm (EM), which is typically used to learn GMMs, fails to cluster the data accurately due to the large number of free parameters in the covariance matrices. We address this weakness by assuming that the mixture model consists of sparse gaussian distributions and leveraging this assumption in a novel algorithm for learning GMMs. Our approach incorporates the graphical lasso procedure for sparse covariance estimation into the EM algorithm for learning GMMs, and by encouraging sparsity, it avoids the problems faced by traditional GMMs. We guarantee convergence of our algorithm and show through experimentation that this procedure outperforms the traditional Expectation Maximization algorithm and other clustering algorithms in the high-dimensional clustering setting.
Robotic Guidance of Flexible Needle for Percutaneous Therapy

Flexible needle insertion for percutaneous therapies is formulated in this paper as a trajectory planning problem of a linear beam, supported by virtual springs. Using this simplified model, the forward and inverse kinematics of the needle is solved analytically, providing a way for simulation and path planning in real-time. Using the inverse kinematics, the required needle basis trajectory can be computed for any desired needle tip path. It is shown that the needle base trajectory is not unique and can be optimized to minimize the lateral pressure of the needle body on the tissue. Experimental results of robotically-assisted flexible needle trajectory tracking are provided.
Highly Fluorescent and Photostable Polymeric Nanofibers as Scaffolds for Cell Interfacing and Long‐Term Tracking

Highly fluorescent polymeric nanofibers fabricated via electrospinning of PCL-DPP-PCL (photostable polycaprolactones-di(thiophene-2-yl)-diketopyrrolopyrrole-photostable polycaprolactones) and commercial PCL mixture show superior photostability and cytocompatibility for long-term tracking of cell-substrate interaction. As a proof of concept, these PCL-DPP-PCL nanofibers enable clear visualization of intricate cell-substrate interactions such as oligodendrocyte myelination.
Antecedent Recovery: Experiments with a Trace Tagger

This paper explores the problem of finding non-local dependencies. First, we isolate a set of features useful for this task. Second, we develop both a two-step approach which combines a trace tagger with a state-of-the-art lexicalized parser and a one-step approach which finds nonlocal dependencies while parsing. We find that the former outperforms the latter because it makes better use of the features we isolate.
The Economic Consequences of Population Growth in Italy: From the 13th Century to 1900: A Discussion on the Mathusian Dynamics

In this paper we investigate the relation between population, real wages and urbanization in the Italian economy during the period 1320-1870. In this period the prevailing conditions were those of a poor, mainly agricultural economy with limited human capital and rudimentary technology. However, these centuries witnessed the considerable growth of urban centers, which was not only a significant demographic phenomenon in itself. The multiplication of such agglomerations had a striking influence on mortality and hence on the general course of the economy in this period. Disease, warfare and famine, which for about 400 years had been the greatest "agents" of demographic dynamics, were the real engine of this economy. One of the main results of this paper is that this "engine", along with the urbanization process and the flows of rural immigrants which fuelled it, had profound, complex implications on productivity in agriculture and on wages and population dynamics.
Low genetic variability in an endangered population of fiddler crab Uca arcuata on Okinawajima Island: analysis of mitochondrial DNA

Restriction fragment length polymorphism analysis was performed on polymerase chain reaction-amplified DNA fragments containing the D-loop, ND2, and CO I genes of fiddler crab Uca arcuata mitochondrial DNA. In total, 316 individuals from six populations in Japan and two populations in Taiwan were analyzed using five restriction endonucleases (Afal, Bcnl, Cfr13l, Haelll and Hinfl), yielding 85 haplotypes. Samples were taken from Nakagusuku Bay, Okinawajima Island, which is the only known distribution of U. arcuata in the Ryukyu Archipelago. The Okinawajima Island population is isolated geographically from others and showed a marked low genetic variability (h=0.2539, π=0.0005) and significant differentiation from other population samples in haplotype composition. We suggest that a substantial decrease in the genetic variability of the Okinawajima Island population was caused by genetic drift under the conditions of small population size and low gene flow from other populations. It is important to conserve the intertidal zone in Nakagusuku Bay for the maintenance of this endangered population.
The FtsLB subcomplex of the bacterial divisome is a tetramer with an uninterrupted FtsL helix linking the transmembrane and periplasmic regions

In Escherichia coli, FtsLB plays a central role in the initiation of cell division, possibly transducing a signal that will eventually lead to the activation of peptidoglycan remodeling at the forming septum. The molecular mechanisms by which FtsLB operates in the divisome, however, are not understood. Here, we present a structural analysis of the FtsLB complex, performed with biophysical, computational, and in vivo methods, that establishes the organization of the transmembrane region and proximal coiled coil of the complex. FRET analysis in vitro is consistent with formation of a tetramer composed of two FtsL and two FtsB subunits. We predicted subunit contacts through co-evolutionary analysis and used them to compute a structural model of the complex. The transmembrane region of FtsLB is stabilized by hydrophobic packing and by a complex network of hydrogen bonds. The coiled coil domain probably terminates near the critical constriction control domain, which might correspond to a structural transition. The presence of strongly polar amino acids within the core of the tetrameric coiled coil suggests that the coil may split into two independent FtsQ-binding domains. The helix of FtsB is interrupted between the transmembrane and coiled coil regions by a flexible Gly-rich linker. Conversely, the data suggest that FtsL forms an uninterrupted helix across the two regions and that the integrity of this helix is indispensable for the function of the complex. The FtsL helix is thus a candidate for acting as a potential mechanical connection to communicate conformational changes between periplasmic, membrane, and cytoplasmic regions.
Structure and function of the Saccharomyces cerevisiae CDC2 gene encoding the large subunit of DNA polymerase III.

Saccharomyces cerevisiae cdc2 mutants arrest in the S‐phase of the cell cycle when grown at the non‐permissive temperature, implicating this gene product as essential for DNA synthesis. The CDC2 gene has been cloned from a yeast genomic library in vector YEp13 by complementation of a cdc2 mutation. An open reading frame coding for a 1093 amino acid long protein with a calculated mol. wt of 124,518 was determined from the sequence. This putative protein shows significant homology with a class of eukaryotic DNA polymerases exemplified by human DNA polymerase alpha and herpes simplex virus DNA polymerase. Fractionation of extracts from cdc2 strains showed that these mutants lacked both the polymerase and proofreading 3′‐5′ exonuclease activity of DNA polymerase III, the yeast analog of mammalian DNA polymerase delta. These studies indicate that DNA polymerase III is an essential component of the DNA replication machinery.
Predation risk drives social complexity in cooperative breeders

Significance It is widely accepted that high predation risk may select for group living, but predation is not regarded as a primary driver of social complexity. This view neglects the important effect of predation on dispersal and offspring survival, which may require cooperation among group members. The significance of predation for the evolution of social complexity can be well illustrated by behavioral and morphological adaptations of highly social animals showing division of labor, such as eusocial insects and cooperatively breeding fishes. By examining the diversity of social organization in a cooperative cichlid in relation to ecological variation, we show that predation risk has the greatest explanatory power of social complexity. This stresses the significance of predation for social evolution. Predation risk is a major ecological factor selecting for group living. It is largely ignored, however, as an evolutionary driver of social complexity and cooperative breeding, which is attributed mainly to a combination of habitat saturation and enhanced relatedness levels. Social cichlids neither suffer from habitat saturation, nor are their groups composed primarily of relatives. This demands alternative ecological explanations for the evolution of advanced social organization. To address this question, we compared the ecology of eight populations of Neolamprologus pulcher, a cichlid fish arguably representing the pinnacle of social evolution in poikilothermic vertebrates. Results show that variation in social organization and behavior of these fish is primarily explained by predation risk and related ecological factors. Remarkably, ecology affects group structure more strongly than group size, with predation inversely affecting small and large group members. High predation and shelter limitation leads to groups containing few small but many large members, which is an effect enhanced at low population densities. Apparently, enhanced safety from predators by cooperative defense and shelter construction are the primary benefits of sociality. This finding suggests that predation risk can be fundamental for the transition toward complex social organization, which is generally undervalued.
Prospective Evaluation of Samarium-153-EDTMP Radionuclide Treatment for Bone Metastases in Patients with Hormone-Refractory Prostate Cancer

Purpose: Bone is a common site of metastatic disease and the most frequent site of metastatic spread in patients with prostate cancer. Most patients with bone metastases complain of bone pains. This pain may be alleviated or eliminated by administration of radiotherapy at the site of metastases. Currently, two forms of radiotherapy administration exist: external-beam irradiation or intravenous administration of bone-seeking therapeutic radiopharmacon such as samarium-153-ethylene-diamino-tetramethylene-phosphonate (EDTMP). This radiopharmacon produces β-particles and concentrates in the areas of enhanced osteoblastic activity. The aim of this study was to assess the efficacy of 153Sm-EDTMP therapy. Materials and Methods: 32 men (aged 50–83, mean 70 years) with bone disseminated hormone-refractory prostate cancer and bone pain received 153Sm-EDTMP. Mean applied dosage was 40 MBq/kg of the patient’s body weight. Karnofsky performance status, pain score (numerical rating scale), analgesic score (WHO) and blood count were evaluated before, and 1 and 3 months after the treatment. Results: Significant pain relief was observed in 44 and 38% of patients, mild relief in 31 and 34% and no effect in 25 and 28% of patients, 1 and 3 months after administration, respectively. Pain palliation was accompanied by an improvement in mobility and a decrease in necessary dosage of analgesics. Mild and transient bone marrow suppression was observed as a side effect of 153Sm-EDTMP treatment. None of the patients showed hematological toxicity grade 4, and only 2 showed grade 3 (NCI CTC). The majority of the patients had hematological toxicity grade 1 or 2. Conclusion: After 153Sm-EDTMP administration, bone pain palliation was observed in 72% of patients for 3 months. Hematological toxicity after 153Sm-EDTMP treatment was mild and transient.
18F-FDG PET-Derived Textural Indices Reflect Tissue-Specific Uptake Pattern in Non-Small Cell Lung Cancer

Purpose Texture indices (TI) calculated from 18F-FDG PET tumor images show promise for predicting response to therapy and survival. Their calculation involves a resampling of standardized uptake values (SUV) within the tumor. This resampling can be performed differently and significantly impacts the TI values. Our aim was to investigate how the resampling approach affects the ability of TI to reflect tissue-specific pattern of metabolic activity. Methods 18F-FDG PET were acquired for 48 naïve-treatment patients with non-small cell lung cancer and for a uniform phantom. We studied 7 TI, SUVmax and metabolic volume (MV) in the phantom, tumors and healthy tissue using the usual relative resampling (RR) method and an absolute resampling (AR) method. The differences in TI values between tissue types and cancer subtypes were investigated using Wilcoxon’s tests. Results Most RR-based TI were highly correlated with MV for tumors less than 60 mL (Spearman correlation coefficient r between 0.74 and 1), while this correlation was reduced for AR-based TI (r between 0.06 and 0.27 except for RLNU where r = 0.91). Most AR-based TI were significantly different between tumor and healthy tissues (pvalues <0.01 for all 7 TI) and between cancer subtypes (pvalues<0.05 for 6 TI). Healthy tissue and adenocarcinomas exhibited more homogeneous texture than tumor tissue and squamous cell carcinomas respectively. Conclusion TI computed using an AR method vary as a function of the tissue type and cancer subtype more than the TI involving the usual RR method. AR-based TI might be useful for tumor characterization.
Evaluating Erp Usage Behavior Of Employees And Its Impact On Their Performance: A Case Of Telecom Sector

Acceptance and use of an information system always remained an important concern for practitioners and theorist. This study explores the factor affecting user behavior toward use of ERP system in developed as well as developing country. Performance expectancy, effort expectancy, social influence, facilitating condition, project communication, training, top management support and self efficacy were found frequently used factors to investigate the ERP usage behavior of employees of a telecom, manufacturing, oil and gas, engineering and government service sector. industry. This study also investigates the impact of behavior toward ERP system usage on the employees’ performance. A questionnaire based survey was administered personally on 300 employees of telecom using ERP in sector In response to the survey, 255 valid responses were received. The response rate was 85%. Among the respondents, 71% were male while 29% were female. The finding indicates that the proposed model over all explains 71% variation in the behavior. While Performance Expectancy, Self Efficacy, Training, and Top Management Support were significant factor while explaining the user behavior toward use of ERP system. Further, the model explains that there is difference about opinion of performance expectancy and effort expectancy related to ERP usage by male and female while effort expectancy related to ERP usage also vary among age and experience groups. Mostly respondents agreed that they likey the idea of usinf ERP syste and they want to become professional in ERP system. Seventy percent respondents say that ERP system has improve their performance in work. behavior toward use of ERP system This research will help the telecom organization management to understand the factors responsible for the employee’s. KeywordsERP, Telecom Industry, ERP usage behavior, Technology Acceptance.
Serum osteoprotegerin level is associated with degree of arteriovenous fistula stenosis in patients with hemodialysis.

AIMS Vascular access dysfunction caused by stenosis is a major complication for hemodialysis (HD) patients. However, the relevant humoral mediators of arteriovenous (AV) access stenosis are still under investigation. The aim of the present study was to evaluate the association between serum fetuin-A, osteoprotegerin (OPG), and heat shock protein (Hsp) 70 concentration with arteriovenous fistula (AVF) patency in HD patients. METHODS Serum fetuin-A, OPG and Hsp70 concentrations were measured in 64 HD patients. Using these data, we studied the association of fetuin-A, OPG and Hsp70 with the degree of AVF stenosis using ultrasonography in HD patients. RESULTS The degree of AVF stenosis was positively correlated with OPG levels (r = 0.411, p = 0.001) and OPG/fetuin-A ratio (r = 0.375, p = 0.002). The levels of OPG and OPG/fetuin-A ratio were statistically higher in the group of AVF stenosis ≥ 11.5%. Stepwise linear regression analyses independently predicted the degree of AVF stenosis on the logarithmic function of the OPG (β = 8.775, standard error = 0.493, p = 0.034) and OPG/fetuin-A ratio (β = 10.325, standard error = 3.247, p = 0.018). CONCLUSIONS Our data demonstrated that OPG and the OPG/fetuin-A ratio correlated with the degree of AVF stenosis in HD patients. In addition, OPG and the OPG/fetuin-A ratio were the most important predictors of the degree of AVF stenosis in HD patients.
A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy

In many of the chemical reactions in living cells, enzymes act as catalysts in the conversion of certain compounds (substrates) into other compounds (products). Comparative analyses of the metabolic pathways formed by such reactions give important information on their evolution and on pharmacological targets (Dandekar et al. 1999). Each of the enzymes that constitute a pathway is classified according to the EC (Enzyme Commission) numbering system, which consists of four sets of numbers that categorize the type of the chemical reaction catalyzed. In this study, we consider that reaction similarities can be expressed by the similarities between EC numbers of the respective enzymes. Therefore, in order to find a common pattern among pathways, it is desirable to be able to use the functional hierarchy of EC numbers to express the reaction similarities. In this paper, we propose a multiple alignment algorithm utilizing information content that is extended to symbols having a hierarchical structure. The effectiveness of our method is demonstrated by applying the method to pathway analyses of sugar, DNA and amino acid metabolisms.
Patient Decision-Making Preference and Physician Decision-Making Style for Contraceptive Method Choice in an Asian Culture: Does Concordance Matter?

This study investigates preferences for patient-physician decision-making in an emerging economy with an Asian culture. A survey of 445 randomly sampled women, aged 20–40 in Hanoi, Vietnam, revealed that pre-consultation attitudes were most positive toward a “shared” decision-making approach with the physician for contraceptive method choice. However, following random assignment to one of three vignettes (passive, shared or autonomous) featuring a young Vietnamese woman reaching a contraceptive method decision with her physician, preference was highest for the “autonomous” approach. Furthermore, discordance between pre-consultation preference for decision-making style and the physician's decision-making style negatively impacted evaluations under some but not all circumstances. This study demonstrates that, despite living in a hierarchic Asian culture, active participation in contraceptive method choice is desired by many urban Vietnamese women. However, there is variation on this dimension and adjusting the physician's style to be concordant with patient preference appears important to maximizing patient satisfaction.
Collaborative Pairwise Detection Schemes for Improving Coverage in WSNs

One of the main applications of Wireless Sensor Networks (WSNs) is area monitoring (e.g., environmental monitoring). In such problems, it is desirable to maximize the area coverage which can be achieved by appropriately positioning the sensors (if possible) and/or by increasing the detection range of the sensors. This paper considers the latter. The emphasis is on pairs of closely spaced sensors that can collaborate in order to increase their collective area coverage. The main contribution of this work is to investigate collaborative detection schemes between a pair of sensor nodes and show that the area coverage achieved by each scheme depends on the distance between the two sensors. For closely spaced sensors, we propose the Enhanced Covariance Detector (ECD) that combines the energy and the covariance information from the two nodes by utilizing two different thresholds (one for the energy test statistic and another for the covariance).