Miracle-dz/UniFAR-FTUs huggingface dataset:
A cell-free protein synthesis system for high-throughput proteomics

We report a cell-free system for the high-throughput synthesis and screening of gene products. The system, based on the eukaryotic translation apparatus of wheat seeds, has significant advantages over other commonly used cell-free expression systems. To maximize the yield and throughput of the system, we optimized the mRNA UTRs, designed an expression vector for large-scale protein production, and developed a new strategy to construct PCR-generated DNAs for high-throughput production of many proteins in parallel. The resulting system achieves high-yield expression and can maintain productive translation for 14 days. Additionally, in the integration of a PCR-directed system for template creation, at least 50 genes can be translated in parallel, yielding between 0.1 and 2.3 mg of protein by one person within 2 days. Assessment of correct protein folding by the products of this high-throughput protein-expression system were performed by enzymatic assays of kinases and by NMR spectroscopic analysis. The cell-free system, reported here, bypasses many of the time-consuming cloning steps of conventional expression systems and lends itself to a robotic automation for the high-throughput expression of proteins.
Conserved role for the Drosophila Pax6 homolog Eyeless in differentiation and function of insulin-producing neurons

Insulin/insulin-like growth factor (IGF) signaling constitutes an evolutionarily conserved pathway that controls growth, energy homeostasis, and longevity. In Drosophila melanogaster, key components of this pathway are the insulin-like peptides (Dilps). The major source of Dilps is a cluster of large neurons in the brain, the insulin-producing cells (IPCs). The genetic control of IPC development and function is poorly understood. Here, we demonstrate that the Pax6 homolog Eyeless is required in the IPCs to control their differentiation and function. Loss of eyeless results in phenotypes associated with loss of insulin signaling, including decreased animal size and increased carbohydrate levels in larval hemolymph. We show that mutations in eyeless lead to defective differentiation and morphologically abnormal IPCs. We also demonstrate that Eyeless controls IPC function by the direct transcriptional control of one of the major Dilps, dilp5. We propose that Eyeless has an evolutionarily conserved role in IPCs with remarkable similarities to the role of vertebrate Pax6 in β cells of the pancreas.
Effects of Food Shortage and Oversupply on Energy Utilization, Histology, and Function of the Gut in Nestling Song Thrushes (Turdus philomelos)

We measured food intake, digestive efficiency, body mass increments, resting metabolic rate (RMR), carcass fat content, size and histological structure of the gut, and the rate of intestinal brush border uptake of l‐proline in song thrush (Turdus philomelos) nestlings subjected to food shortage or food surplus under laboratory conditions. We assigned nestlings between 3 and 7 d of age to one of the following treatments: (1) food restriction, which resulted in a slowed growth at the rate found in undernourished, wild nestlings; (2) overfeeding, which totally suppressed begging; and (3) intermediate feeding. Threefold differences in energy consumption caused fivefold differences in body mass increments of the nestlings. Despite this, body mass–corrected RMR and intestinal mass were not affected by the feeding regime. The energy content of fecal output was highest in food‐restricted birds, while their carcass fat content was lowest among treatment groups. Intestinal uptake rates of l‐proline were low in the overfed and intermediate‐fed young but significantly increased in the food‐restricted birds, who attempted to maximize their rates of growth and development within the restrictive limits set by feeding regime. We noted a marked decrease of intestinal villi height in overfed birds as compared to intermediate‐fed and food‐restricted nestlings. We conclude that song thrush nestlings are characterized by a limited plasticity of their developmental program, which prohibits overfed nestlings from significantly up‐regulating their gut function to accommodate increased food intake. This suggests that they already grew at a rate close to their physiological maximum. We suggest two interpretations: (1) under natural conditions, song thrush nestlings do not face frequent, unpredictable fluctuations in food abundance that could select for developmental plasticity, or (2) strong selection for uniform adult phenotypes prevents flexible developmental trajectories, which would result in a diversity of adult phenotypes.
APS-FeW: The Second Order Enhancement for TCP over Multihop 802.11 Networks

TCP is a reliable transport protocol tuned to perform well over traditional wired networks. Although it performs well for wired networks, TCP's implicit assumption that any packet loss is due to congestion is not valid any longer in mobile ad hoc networks. It is observed that TCP induces the over-action of routing protocol and reduces the performance of the connection. Fraction window increment (FeW) scheme for TCP improves the connection performance by limiting TCP's aggressiveness. But to some extent, this limitation is too strict in that it eliminates the possibility to deliver more bytes under the same congestion window. To solve this problem, we propose an adaptive packet size (APS) scheme to work on top of FeW for TCP. The proposed scheme utilizes the advantages of both legacy TCP and FeW to achieve high performance over multihop 802.11 networks. Extensive simulation results demonstrate that APS over FeW outperforms FeW alone by 10 -25 % according to different scenarios, e.g., chain-topology, grid-topology, and random-topology with mobility.
An ultrasonographic evaluation of masseter muscle thickness in different dentofacial patterns.

OBJECTIVES The aim of this study is to compare the masseter muscle thickness in different vertical dentofacial patterns and identify the possible sexual dimorphism and also to correlate masseter muscle thickness with craniofacial morphology using cephalometric parameters. MATERIALS AND METHODS The masseter muscle thickness was measured using ultrasonography in 60 subjects (30 females and 30 males). Standardized lateral and posteroanterior cephalograms were taken to determine the facial morphology. The subjects were divided into three vertical pattern groups (I, II, and III) according to their Jarabak ratio: hypodivergent ( n = 20), normodivergent (n = 20), and hyperdivergent (n = 20). The sample was further subdivided into males and female subgroups. RESULTS Masseter muscle thickness relaxed (MMTR) in hypodivergent group was 13.94 ± 1.51. Mean value of MMTR in normodivergent group was 12.53 ± 1.21 and the MMTR in hyperdivergent group was 11.13 ± 1.18. The mean value of masseter muscle thickness contracted (MMTC) in hypodivergent group was 15.46 ± 1.33. Mean value of MMTC in normodivergent group was 13.81 ± 1.38 and the mean value of MMTC in hyperdivergent group was 12.27 ± 1.26. MMTC showed a significant, negative correlation with mandibular plane angle and gonial angle. Posterior facial height, symphysis width, intermolar width of maxillary first molars, maxillary width, and facial width (bizygomatic width) showed significant ( P < 0.05 or P < 0.01) positive correlation. CONCLUSION The masseter muscle thickness varied among the three vertical dentofacial patterns and sexual dimorphism also existed except in the hyperdivergent group. Masseter muscle thickness was found to be negatively correlated to vertical facial pattern and positively associated with transverse craniofacial morphology.
Automated vocal emotion recognition using phoneme class specific features

Methods for automated vocal emotion recognition often use acoustic feature vectors that are computed for each frame in an utterance, and global statistics based on these acoustic feature vectors. However, at least two considerations argue for usage of phoneme class specific features for emotion recognition. First, there are well-known effects of phoneme class on some of these features. Second, it is plausible that emotion influences the speech signal in ways that differ between phoneme classes. A new method based on the concept of phoneme class specific features is proposed in which different features are selected for regions associated with different phoneme classes and then optimally combined, using machine learning algorithms. A small but significant improvement was found when this method was compared with an otherwise identical method in which features were used uniformly over different phoneme classes.
Call for Papers : Cell Signaling : Proteins , Pathways and Mechanisms Delivery of a protein transduction domain-mediated Prdx 6 protein ameliorates oxidative stress-induced injury in human and mouse neuronal cells

Singh SP, Chhunchha B, Fatma N, Kubo E, Singh SP, Singh DP. Delivery of a protein transduction domain-mediated Prdx6 protein ameliorates oxidative stress-induced injury in human and mouse neuronal cells. Am J Physiol Cell Physiol 310: C1–C16, 2016. First published October 7, 2015; doi:10.1152/ajpcell.00229. 2015. —Oxidative stress or reduced expression of naturally occurring antioxidants during aging has been identified as a major culprit in neuronal cell/tissue degeneration. Peroxiredoxin (Prdx) 6, a protective protein with GSH peroxidase and acidic calcium-independent phospholipase A2 activities, acts as a rheostat in regulating cellular physiology by clearing reactive oxygen species (ROS) and thereby optimizing gene regulation. We found that under stress, the neuronal cells displayed reduced expression of Prdx6 protein and mRNA with increased levels of ROS, and the cells subsequently underwent apoptosis. Using Prdx6 fused to TAT transduction domain, we showed evidence that Prdx6 was internalized in human brain cortical neuronal cells, HCN-2, and mouse hippocampal cells, HT22. The cells transduced with Prdx6 conferred resistance against the oxidative stress inducers paraquat, H2O2, and glutamate. Furthermore, Prdx6 delivery ameliorated damage to neuronal cells by optimizing ROS levels and overstimulation of NFB. Intriguingly, transduction of Prdx6 increased the expression of endogenous Prdx6, suggesting that protection against oxidative stress was mediated by both extrinsic and intrinsic Prdx6. The results demonstrate that Prdx6 expression is critical to protecting oxidative stress-evoked neuronal cell death. We propose that local or systemic application of Prdx6 can be an effective means of delaying/postponing neuronal degeneration.
A Review of Case Management for People Who Are Homeless : Implications for Practice , Policy , and Research

Case management programs for homeless people have proliferated since the 1980s but some have questioned the meaning and clarity of the term case management while others have questioned its effectiveness for serving clients. This paper first attends to conceptual issues, identifying primary functions and process variables for understanding and describing case management services. The paper next describes models and approaches to case management for various client subgroups and specialty areas. The paper also reviews the empirical literature on homelessness and case management, especially as it relates to treatment effectiveness and critical factors. Several conclusions are postulated, including that some case management approaches, especially assertive community treatment (ACT), are effective for helping people who are homeless with severe mental illness; frequent service contact is a critical ingredient leading to positive treatment retention and housing outcomes; case management is more effective with some clients than others. A number of gaps in our knowledge of case management are also identified. The final section of the paper presents recommendations on exemplary practices. These include recommendations related to critical staff skills and abilities, service principles, case management models, and organizational practices. Lessons for Practitioners, Policy Makers, and Researchers Recommendations for homeless case management practitioners include focusing service delivery efforts upon: • Conducting assertive, community-based outreach; • Nurturing trusting, caring relationships with clients; • Respecting client autonomy; • Prioritizing client self-determined needs; • Providing clients with active assistance to obtain needed resources; • Maintaining small case loads; and • Implementing ACT approaches. The federal government is also encouraged to promote exemplary practices through knowledge dissemination, advocacy, and financing actions and to promote new research and knowledge on case management services for people who are homeless.
Numerical simulation of the effect of the ion-driven wind on flame stability

When an electric field is applied to a flame, the charged species present in the flame front undergo a volumetric electric force, which changes the flow dynamics in the flame front region. This modification of the flow can contribute to a better stabilization of a diffusion lifted flame. All studies interested in combustion interaction with an electric field have shown improvements in combustion stabilisation. However, because of the disparities among results, it is difficult to draw conclusions on what is the key physical phenomenon responsible for stabilisation improvement. Numerical simulation may be a valuable approach for answering this question. Until now, only few studies have proposed modelling approaches for combustion in the presence of an electric field [1, 4]. In these numerical studies, the negative ions are overlooked, and only the movement of positive ions under the effect of a direct electric field (DC) was examined. In the present paper, the simplified mathematical model [4] is improved in order to include anions. The equations of aerothermochemistry coupled with transport equations for positive ion, negative ion and electron concentrations along with a Poisson equation for the potential electric field are solved. This model does not incorporate possible effects of the electric field on the combustion chemistry and accounts solely for ion-driven wind effects. The objectives of the study are: (1) to assess the ability of the ion-driven wind phenomenon to influence flame stabilisation, when both positive and negative ions are considered. (2) to provide a numerical tool for predicting the behaviour of the flame under the effect of an external electric field. In this context, a generic configuration, already used in [4], representative of a lifted diffusion methane/air laminar flame is used to analyse the mechanism of stabilisation of the flame in the presence of an applied electric field. This configuration is schematised in fig. 1.
The role of bone traumatization in the initiation of proximal deep vein thrombosis during cemented hip replacement surgery in pigs

Hip arthroplasty is associated with a high frequency of postoperative solitary proximal deep vein thrombosis which seems most frequently observed when bone cement is used for prosthesis fixation. Eighteen pigs underwent hemiarthroplasty, eight with cement-fixed prostheses and eight with non-cement prosthesis installation. Levels of thrombin—antithrombin (TAT) complexes, tissue plasminogen activator (t-PA) activity and plasminogen activator inhibitor 1 (PAI-1) activity were determined in femoral vein blood from both limbs during and after surgery. On the operated side, TAT increased during bone traumatization followed by a substantial rise in t-PA activity and a gradual decline in PAI-1 activity. This indicates a local per-and post-operative sequential activation of coagulation and fibrinolysis followed by a fibrinolytic shutdown, all reflected in femoral vein blood on the operated side. In the animals receiving noncemented hip prostheses, the same pattern of activation of coagulation and fibrinolysis occurred on the operated side. This was, however, less marked than with the cement-fixed prostheses. Postoperative scanning electron microscopic (SEM) examination of the femoral veins showed thrombi on the operated side in 62% of the animals in the cement group and 25% in the non-cement group. In an additional study with eight animals undergoing cement-anchored hip prosthesis operations the levels of TAT, t-PA and PAI-I were analysed in femoral vein blood, mixed venous blood and arterial blood. Significantly higher levels were found in femoral vein blood compared with mixed venous blood while no significant change was found in arterial blood compared with mixed venous blood. The hyperthermia induced by curing bone cement was effectively conducted by the implanted prosthesis and did not seem to exert major influence on the activation of coagulation. Extreme rotation of the limbs during surgery did not in itself induce visible vein wall damage as judged by SEM. These studies indicate that traumatization of bone marrow during hip surgery induce a marked local activation of coagulation and a high incidence of deep vein thrombosis in proximal veins, in particular if bone cement is used for prosthesis fixation.
Measurement of Spurious Voltages in ZnO Piezoelectric Nanogenerators

The recent development and commercialization of microelectromechanical systems (MEMS)/nanoelectromechanical systems (NEMS) has brought the related challenge of independently powering such systems. The concept of the nanogenerator (NG) has shown potential for harvesting energy from the ambient environment to power MEMS/NEMS. Kinetic energy harvesting NGs based on the piezoelectric properties of ZnO nanowires have attracted much interest. In this paper, we have fabricated hydrothermally synthesized ZnO-based NGs following the procedures standardized in the published literature. Likewise, reference NGs without ZnO piezoelectric material were fabricated in parallel with the ZnO NGs. The voltage output of both the ZnO NG and the reference NG was measured given a 10-Hz cyclic vertical load. Unexpectedly, both the ZnO and the reference NG were found to produce 3 mV with 0.451 N of load. A finite-element model was created to determine that the voltage potential of the NG should be about 1 mV with the given load. A possible explanation for this unexpected behavior is that the measured signals are not entirely piezoelectric in nature. Rather, the signals recorded from the NGs may be some alternate phenomenon, such as the triboelectric, flexoelectric, or electret effect.
Combining Suppression Subtractive Hybridization and Microarrays To Map the Intraspecies Phylogeny of Flavobacteriumpsychrophilum

ABSTRACT Reciprocal subtractive libraries were prepared for two strains of Flavobacteriumpsychrophilum, one virulent and the other avirulent in a trout challenge model. Unique clones were sequenced and their distribution assessed among 34 strains. The analysis showed that F. psychrophilum is composed of two genetic lineages, possibly reflecting host specificity.
A combined nutritional-behavioral-physical activity intervention for the treatment of childhood obesity – a 7-year summary

Abstract We assessed the effect of a weight management program on body weight, body mass index (BMI), BMI percentile, and fitness in obese children and adolescents. The study was designed as a longitudinal, non-randomized, clinical experience of 3, 6, and 12 months combined dietary-behavioral-exercise intervention. Seven hundred and forty-nine obese children (age, 6–16 years) participated in a 3 months program. Three hundred and fifty-nine of them completed a 6 months intervention and 147 completed a 1 year intervention. Sixty-seven age- and maturity-matched obese children who did not participate in the structured program served as controls. Body weight, BMI, and fitness were evaluated at baseline, and after 3, 6, and 12 months intervention. Body weight, BMI, and BMI percentiles were significantly reduced (p<0.05) and endurance time significantly increased (p<0.0005) following the 3 months intervention. Obese children who continued the program for 6 months maintained decreases in BMI percentiles and further improved endurance time. In contrast, obese children in the control group gained weight, increased their BMI, and had a less significant improvement in fitness. Parental obesity (both parents), degree of obesity (BMI >97%), and more than one prior weight loss attempt were associated with lower decreases, whereas sex and pubertal status had no influence, on BMI percentiles changes. Children without parental overweight had significantly greater decreases in BMI compared with children with both parents showing obesity. In summary, a combined, structured multidisciplinary intervention for childhood obesity led to decreased body weight, BMI, and BMI percentiles, and to improved fitness.
Visual impairment in a Taiwanese population: Prevalence, causes, and socioeconomic factors

Abstract PURPOSE We sought to estimate the prevalence of visual impairment among an elderly population in urban Taiwan, determine the causes of visual impairment, and gain information about certain socioeconomic factors associated with visual impairment. METHODS A population-based survey of ocular diseases in residents aged 50 years or older was conducted in Peitou Precinct, Taipei, Taiwan. All participants underwent a comprehensive ophthalmic examination, including visual acuity measurement, using standardized protocols. Demographic data, marital status, employment status, and educational level were gathered through an interview. RESULTS A total of 2034 participants completed the visual acuity measurements. The prevalence of visual impairment (defined as best-corrected visual acuity in the better eye <6/18) among this population was 2.75% (95% confidence intervals: 2.04%–3.46%). Three major causes of visual impairment were cataract (30.4%), high myopic macular degeneration (25.0%), and age-related macular degeneration (14.3%). In multivariate analysis, age was positively correlated with visual impairment (P < 0.001), and higher education level was associated with a significant decrease in the odds of being visually impaired (P < 0.001). No relation was found between visual impairment and sex, or marital and employment status. CONCLUSIONS This study provides the first information about the prevalence and causes of visual impairment in Taiwan, and identifies age and educational level as the most important factors related to visual impairment. Additional educational programs should be developed to improve individual awareness of age-related ocular diseases and the availability of current ophthalmic intervention.
Reputation Systems : The Effects of Feedback Comments and Reactions on Building and Rebuilding Trust in Online

Previous research on reputation systems has primarily focused on the trust building function of reputation systems. The current research also addresses the trust rebuilding function of reputation systems, specifically, the role of the short text comments given in reaction to negative feedback. Online markets are noisy environments; rebuilding trust is therefore often necessary. The results of two experimental studies among actual eBay users show that the text comments accompanying negative feedback are influential towards trustworthiness judgments. It also makes a difference whether a trust violation is perceived as competence-based or morality-based. Moreover, plain apologies were observed to be more successful in repairing trust than denials. The effects were mediated by perceived believability of the comments. Thus, to avoid the detrimental effects of noise on trust, operators of online market places should encourage text feedback comments and reactions. keywords: reputation systems, trust, trust reparation, apology, denial to appear in Int. J. of Electronic Commerce (2009)