Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular shape analysis based upon the morse-smale complex and the connolly function

Docking is the process by which two or several molecules form a complex. Docking involves the geometry of the molecular surfaces, as well as chemical and energetical considerations. In the mid-eighties, Connolly proposed a docking algorithm matching surface knobs with surface depressions. Knobs and depressions refer to the extrema of the Connolly function, which is defined as follows. Given a surface M bounding a three-dimensional domain X, and a sphere S centered at a point p of M, the Connolly function is equal to the solid angle of the portion of S containing within X.We recast the notions of knobs and depressions in the framework of Morse theory for functions defined over two-dimensional manifolds. First, we study the critical points of the Connolly function for smooth surfaces. Second, we provide an efficient algorithm for computing the Connolly function over a triangulated surface. Third, we introduce a Morse-Smale decomposition based on Forman's discrete Morse theory, and provide an O(n log n) algorithm to construct it. This decomposition induces a partition of the surface into regions of homogeneous flow, and provides an elegant way to relate local quantities to global ones--from critical points to Euler's characteristic of the surface. Fourth, we apply this Morse-Smale decomposition to the discrete gradient vector field induced by Connolly's function, and present experimental results for several mesh models.
A Methodology for Transforming an Existing Distribution Network Into a Sustainable Autonomous Micro-Grid

A distribution network with renewable and fossil-based resources can be operated as a micro-grid, in autonomous or nonautonomous modes. Autonomous operation of a distribution network requires cautious planning. In this context, a detailed methodology to develop a sustainable autonomous micro-grid is presented in this paper. The proposed methodology suggests novel sizing and siting strategies for distributed generators and structural modifications for autonomous micro-grids. The optimal sites and corresponding sizes of renewable resources for autonomous operation are obtained using particle swarm optimization and genetic algorithm-based optimization techniques. Structural modifications based on ranking of buses have been attempted for improving the voltage profile of the system, resulting in reduction of real power distribution losses. The proposed methodology is adopted for a standard 33-bus distribution system to operate as an autonomous micro-grid. Results confirm the usefulness of the proposed approach in transforming an existing radial distribution network into an autonomous micro-grid.
It Is All About Being Popular: The Effects of Need for Popularity on Social Network Site Use

Prior research on predictors of social network site (SNS) use has mainly focused on the Big Five, narcissism, and self-esteem. Results have been inconsistent, and variance explained was rather low. Need for popularity (NfP) might be a better predictor of SNS use, because SNSs are ideal venues for people with a high NfP. Study 1 tested NfP, self-esteem, need to belong, entitlement, and vanity as predictors for a range of SNS behaviors; Study 2 replaced entitlement and vanity with narcissism and added the Big Five as predictors. SNS behaviors assessed were grooming, strategic self-presentation, profile enhancement, disclosure of feelings, routine use of SNS, and number of friends. Results showed that NfP was the strongest and most consistent predictor of SNS behaviors. This pattern indicates that NfP plays an important role in SNSs.
Interaction of NANOS2 and NANOS3 with different components of the CNOT complex may contribute to the functional differences in mouse male germ cells

ABSTRACT NANOS2 and NANOS3 belong to the Nanos family of proteins that contain a conserved zinc finger domain, which consists of two consecutive CCHC-type zinc finger motifs, and contribute to germ cell development in mice. Previous studies indicate that there are redundant and distinct functions of these two proteins. NANOS2 rescues NANOS3 functions in the maintenance of primordial germ cells, whereas NANOS3 fails to replace NANOS2 functions in the male germ cell pathway. However, the lack of a conditional allele of Nanos3 has hampered delineation of each contribution of NANOS2 and NANOS3 to the male germ cell pathway. In addition, the molecular mechanism underlying the distinct functions of these proteins remains unexplored. Here, we report an unexpected observation of a transgenic mouse line expressing a NANOS2 variant harboring mutations in the zinc finger domain. Transcription of Nanos2 and Nanos3 was strongly compromised in the presence of this transgene, which resulted in the mimicking of the Nanos2/Nanos3 double-null condition in the male gonad. In these transgenic mice, P-bodies involved in RNA metabolism had disappeared and germ cell differentiation was more severely affected than that in Nanos2-null mice, indicating that NANOS3 partially substitutes for NANOS2 functions. In addition, similar to NANOS2, we found that NANOS3 associated with the CCR4-NOT deadenylation complex but via a direct interaction with CNOT8, unlike CNOT1 in the case of NANOS2. This alternate interaction might account for the molecular basis of the functional redundancy and differences in NANOS2 and NANOS3 functions.
Effect of organoclay platelets on the mechanical properties of wood–plastic composites formulated with virgin and recycled polypropylene

Abstract This study investigated the effects of organoclay platelet contents (0, 3 and 5 wt%) and polypropylene type (virgin and recycled) on the mechanical properties of polypropylene/wood flour composites. Composite samples were made by melt compounding and consequent injection moulding. The tensile, flexural and impact properties of resultant composites were determined. X-ray diffraction (XRD) analysis of composites with 3 and 5% nanoclay content was also conducted. The results indicated that tensile and flexural properties of the composites increased with the addition of nanoclay particles up to 3 wt% and decreased thereafter. The impact strength of the composites, however, decreased with the incorporation of nanoclay. The mechanical properties of the recycled polypropylene-based nanocomposites were statistically comparable with those based on virgin polypropylene. XRD analysis revealed that the degree of intercalation in the nanocomposites containing 3% nanoclay was higher than in those containing 5%. Based on these results, it can be concluded that recycled polypropylene could be used instead of virgin polypropylene in the production of value-added products with no significant adverse effects on the mechanical properties.
Social capital: implications for development theory, research, and policy

In the 1990s the concept of social capital defined here as the norms and networks that enable people to act collectively enjoyed a remarkable rise to prominence across all the social science disciplines. The authors trace the evolution of social capital research as it pertains to economic development and identify four distinct approaches the research has taken : communitarian, networks, institutional, and synergy. The evidence suggests that of the four, the synergy view, with its emphasis on incorporating different levels and dimensions of social capital and its recognition of the positive and negative outcomes that social capital can generate, has the greatest empirical support and lends itself best to comprehensive and coherent policy prescriptions. The authors argue that a significant virtue of the idea of and discourse on social capital is that it helps to bridge orthodox divides among scholars, practitioners, and policymakers.
Towards Bottom-Up Analysis of Social Food

Social media provide a wealth of information for research into public health by providing a rich mix of personal data, location, hashtags, and social network information. Among these, Instagram has been recently the subject of many computational social science studies. However despite Instagram's focus on image sharing, most studies have exclusively focused on the hashtag and social network structure. In this paper we perform the first large scale content analysis of Instagram posts, addressing both the image and the associated hashtags, aiming to understand the content of partially-labelled images taken in-the-wild and the relationship with hashtags that individuals use as noisy labels. In particular, we explore the possibility of learning to recognise food image content in a data driven way, discovering both the categories of food, and how to recognise them, purely from social network data. Notably, we demonstrate that our approach to food recognition can often achieve accuracies greater than 70% in recognising popular food-related image categories, despite using no manual annotation. We highlight the current capabilities and future challenges and opportunities for such data-driven analysis of image content and the relation to hashtags.
Haplotype Kernel Association Test as a Powerful Method to Identify Chromosomal Regions Harboring Uncommon Causal Variants

For most complex diseases, the fraction of heritability that can be explained by the variants discovered from genome‐wide association studies is minor. Although the so‐called “rare variants” (minor allele frequency [MAF] < 1%) have attracted increasing attention, they are unlikely to account for much of the “missing heritability” because very few people may carry these rare variants. The genetic variants that are likely to fill in the “missing heritability” include uncommon causal variants (MAF < 5%), which are generally untyped in association studies using tagging single‐nucleotide polymorphisms (SNPs) or commercial SNP arrays. Developing powerful statistical methods can help to identify chromosomal regions harboring uncommon causal variants, while bypassing the genome‐wide or exome‐wide next‐generation sequencing. In this work, we propose a haplotype kernel association test (HKAT) that is equivalent to testing the variance component of random effects for distinct haplotypes. With an appropriate weighting scheme given to haplotypes, we can further enhance the ability of HKAT to detect uncommon causal variants. With scenarios simulated according to the population genetics theory, HKAT is shown to be a powerful method for detecting chromosomal regions harboring uncommon causal variants.
A split-aperture transmit beamforming technique with phase coherence grating lobe suppression

A small element-to-element pitch (~.5λ) is conventionally required for phased array ultrasound transducers to avoid large grating lobes. This constraint can introduce many fabrication difficulties, particularly in the development of high-frequency phased arrays at operating frequencies greater than 30 MHz. In this paper, a new transmit beamforming technique along with sign coherence factor (SCF) receive beamforming is proposed to suppress grating lobes in large-pitch phased-array transducers. It is based on splitting the transmit aperture (N elements) into N/K transmit elements and receive beamforming on all N elements to reduce the temporal length of the transmit grating lobe signal. Therefore, the use of synthetic aperture beamforming, which can introduce relative phase distortions between the echoes received over many transmit events, can be avoided. After each transmit-receive event, the received signals are weighted by the calculated SCF to suppress the grating lobes. After pulsing all sub-apertures, the RF signals are added to generate one line of the image. Simulated 2-way radiation patterns for different K values show that grating lobes can be suppressed significantly at different steering angles. Grating lobes can be suppressed by approximately 20 dB with K = 2 at steering angles greater than 25° and an element pitch greater than 0. 75λ. A technique for determining the optimal transmit sub-apertures has been developed.
Information Processing Letters a Note on Element-wise Matrix Sparsification via a Matrix-valued Bernstein Inequality

a r t i c l e i n f o a b s t r a c t Given a matrix A ∈ R n×n , we present a simple, element-wise sparsification algorithm that zeroes out all sufficiently small elements of A and then retains some of the remaining elements with probabilities proportional to the square of their magnitudes. We analyze the approximation accuracy of the proposed algorithm using a recent, elegant non-commutative Bernstein inequality, and compare our bounds with all existing (to the best of our knowledge) element-wise matrix sparsification algorithms.
Nocturnal Regrets and Insomnia in Elderly People

Despite their importance for general health, emotion-related factors have rarely been considered in the etiology of late-life insomnia. This study explored the relations between impulsivity, regret experiences, use of different thought-control strategies, and insomnia severity in a sample of older adults whose age ranged from 51 to 98 years. Results revealed that: (a) regret frequency varies across the hours of the day, with a peak in the evening when people are trying to fall asleep; (b) individuals scoring high on impulsive urgency are particularly prone to experience nocturnal regrets; (c) nocturnal regrets are associated with insomnia severity, independently of other well-known risk factors such as depression, sleep-interfering medical conditions, and medications; and (d) the thought-control strategies of self-attacking, thought suppression, and worry are positively associated with the frequency of nocturnal regrets and insomnia severity. These findings indicate that dysfunctional regret regulation plays an important role for sleep disturbances in elderly people.
Use of Thioredoxin as a Reporter To Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition Particle-Dependent Translocation

ABSTRACT We have previously reported that the DsbA signal sequence promotes efficient, cotranslational translocation of the cytoplasmic protein thioredoxin-1 via the bacterial signal recognition particle (SRP) pathway. However, two commonly used signal sequences, those of PhoA and MalE, which promote export by a posttranslational mechanism, do not export thioredoxin. We proposed that this difference in efficiency of export was due to the rapid folding of thioredoxin in the cytoplasm; cotranslational export by the DsbA signal sequence avoids the problem of cytoplasmic folding (C. F. Schierle, M. Berkmen, D. Huber, C. Kumamoto, D. Boyd, and J. Beckwith, J. Bacteriol. 185:5706-5713, 2003). Here, we use thioredoxin as a reporter to distinguish SRP-dependent from non-SRP-dependent cleavable signal sequences. We screened signal sequences exhibiting a range of hydrophobicity values based on a method that estimates hydrophobicity. Successive iterations of screening and refining the method defined a threshold hydrophobicity required for SRP recognition. While all of the SRP-dependent signal sequences identified were above this threshold, there were also a few signal sequences above the threshold that did not utilize the SRP pathway. These results suggest that a simple measure of the hydrophobicity of a signal sequence is an important but not a sufficient indicator for SRP recognition. In addition, by fusing a number of both classes of signal sequences to DsbA, we found that DsbA utilizes an SRP-dependent signal sequence to achieve efficient export to the periplasm. Our results suggest that those proteins found to be exported by SRP-dependent signal sequences may require this mode of export because of their tendency to fold rapidly in the cytoplasm.
Attachment narratives and behavioral and emotional symptoms in an ethnically diverse, at-risk sample.

OBJECTIVE To examine the clinical correlates and predictions from attachment narratives in a sample of early school-age children from a high psychosocial risk, ethnically diverse sample. METHOD A total of 113 children were assessed using the Manchester Child Attachment Story Task, a semistructured assessment of children's attachment representations. Parents and teachers provided data using the Strengths and Difficulties Questionnaire. Peer nominations of popularity and antisocial behavior were also obtained. RESULTS Significant associations that were modest to moderate in magnitude were obtained between attachment narrative scales indexing security, coherence, and disorganization with multiple indices of children's behavioral and emotional adjustment, prosocial behavior and competence; these associations held across ethnic groups and were independent of psychosocial risk. CONCLUSIONS The findings build on and extend support for the use of attachment narrative assessments in the clinical context and demonstrate their applicability and validity across a broad range of ethnicity and social contexts.
Biochemical and in vivo properties of commercial virus‐inactivated factor VIII concentrates

The following commercial virus‐inactivated factor VIII concentrates were studied in vitro: AHF‐Kabi and Octonativ, KabiVitrum; Hemofil T, Hyland; Factorate HP and Monoclate, Armour; Nordiocto, Nordisk Gentofte (dry heated); Kryobulin TIM3, Immuno (steam treated); Profilate, Alpha (heated as dry material slammed in heptane); Hemate P, Behring (wet heated) and Octa‐V.I. , Octapharma (solvent/detergent treated). The concentration of VIII:C was lowest in AHF‐Kabi, whereas it ranged from 24 to 53 IU/ml in the high purity concentrates, except for Monoclate in which it ranged from 91–128 IU/ml. All concentrates but Octa‐V.I. had higher values for VIILAg than for VIII:C. von Willebrand factor with normal distribution of multimers could only be demonstrated in AHF‐Kabi and Hemate P. In vivo studies were performed in 12 severe hemophiliacs. Recovery and half‐life of VIILC did not differ between the various concentrates. Hemate P was given to 5 patients with severe von Willebrand's disease, in all of whom a correction of the hemostatic defect was seen.
System Identification and Closed-Loop Control of End-Tidal CO$_{\bf 2}$ in Mechanically Ventilated Patients

This paper presents a systematic approach to system identification and closed-loop control of end-tidal carbon dioxide partial pressure (PETCO2) in mechanically ventilated patients. An empirical model consisting of a linear dynamic system followed by an affine transform is proposed to derive a low-order and high-fidelity representation that can reproduce the positive and inversely proportional dynamic input-output relationship between PETCO2 and minute ventilation in mechanically ventilated patients. The predictive capability of the empirical model was evaluated using experimental respiratory data collected from 18 mechanically ventilated human subjects. The model predicted PETCO2 response accurately with a root-mean-squared error of 0.22 ± 0.16 mmHg and a coefficient of determination r2 of 0.81 ± 0.18 (mean ± SD) when a second-order rational transfer function was used as its linear dynamic component. Using the proposed model, a closed-loop control method for PETCO2 based on a proportional-integral (PI) compensator was proposed by systematic analysis of the system root locus. For the 18 mechanically ventilated patient models identified, the PI compensator exhibited acceptable closed-loop response with a settling time of 1.27 ± 0.20 min and a negligible overshoot (0.51 ± 1.17%), in addition to zero steady-state PETCO2 set point tracking. The physiologic implication of the proposed empirical model was analyzed by comparing it with the traditional multicompartmental model widely used in pharmacological modeling.
Power/Ground Network and Floorplan Cosynthesis for Fast Design Convergence

As technology advances, the metal width decreases while the global wire length increases. This trend makes the resistance of the power wire increase substantially. Furthermore, the threshold voltage scales nonlinearly, raising the ratio of the threshold voltage to the supply voltage and making the voltage (IR) drop in the power/ground (P/G) network a serious problem in modern IC design. Traditional P/G network-analysis methods are often very computationally expensive, and it is, thus, not feasible to cosynthesize P/G network with floorplan. To make the cosynthesis feasible, we need not only an efficient, effective, and flexible floorplanning algorithm but also a very efficient yet sufficiently accurate P/G network-analysis method. In this paper, we present a method for floorplan and P/G network cosynthesis based on an efficient P/G network-analysis scheme and the B*-tree floorplan representation. We integrate the cosynthesis into a commercial design flow to develop an effective power-integrity (IR drop)-driven design methodology. Experimental results based on a real-world circuit design and the MCNC benchmarks show that our design methodology successfully fixes the IR-drop errors earlier at the floorplanning stage and, thus, enables the single-pass design convergence
Polyamine depletion inhibits apoptosis following blocking of survival pathways in human chondrocytes stimulated by tumor necrosis factor‐α

Chondrocyte apoptosis can be an important contributor to cartilage degeneration, thereby making it a potential therapeutic target in articular diseases. To search for new approaches to limit chondrocytic cell death, we investigated the requirement of polyamines for apoptosis favored by tumor necrosis factor‐α (TNF), using specific polyamine biosynthesis inhibitors in human chondrocytes. The combined treatment of C‐28/I2 chondrocytes with TNF and cycloheximide (CHX) resulted in a prompt effector caspase activation and internucleosomal DNA fragmentation. Pre‐treatment of chondrocytes with α‐difluoromethylornithine (DFMO), an ornithine decarboxylase (ODC) inhibitor, markedly reduced putrescine and spermidine content as well as the caspase‐3 activation and DNA fragmentation induced by TNF and CHX. DFMO treatment also inhibited the increase in effector caspase activity provoked by TNF plus MG132, a proteasome inhibitor. DFMO decreased caspase‐8 activity and procaspase‐8 content, an apical caspase essential for TNF‐induced apoptosis. Although DFMO increased the amount of active, phosphorylated Akt, inhibitors of the Akt pathway failed to restore the TNF‐induced increase in caspase activity blunted by DFMO. DFMO also reduced the increase in caspase activity induced by staurosporine, but in this case Akt inhibition prevented the DFMO effect. Pre‐treatment with CGP 48664, an S‐adenosylmethionine decarboxylase (SAMDC) inhibitor markedly reduced spermidine and spermine levels, and provoked effects similar to those caused by DFMO. Finally DFMO was effective even in primary osteoarthritis (OA) chondrocyte cultures. These results suggest that the intracellular depletion of polyamines in chondrocytes can inhibit both the death receptor pathway by reducing the level of procaspase‐8, and the apoptotic mitochondrial pathway by activating Akt. © 2005 Wiley‐Liss, Inc.