Miracle-dz/UniFAR-FTUs huggingface dataset:
FamClash: A method for ranking the activity of engineered enzymes

This article introduces the computational procedure FamClash for analyzing incompatibilities in engineered protein hybrids by using protein family sequence data. All pairs of residue positions in the sequence alignment that conserve the property triplet of charge, volume, and hydrophobicity are first identified, and significant deviations are denoted as residue–residue clashes. This approach moves beyond earlier efforts aimed at solely classifying hybrids as functional or nonfunctional by correlating the rank ordering of these hybrids based on their activity levels. Experimental testing of this approach was performed in parallel to assess the predictive ability of FamClash. As a model system, single-crossover ITCHY (incremental truncation for the creation of hybrid enzymes) libraries were prepared from the Escherichia coli and Bacillus subtilis dihydrofolate reductases, and the activities of functional hybrids were determined. Comparisons of the predicted clash map as a function of crossover position revealed good agreement with activity data, reproducing the observed V shape and matching the location of a local peak in activity.
Returning to the workforce after retiring: a job demands, job control, social support perspective on job satisfaction

Despite growing interest in the aging of the workforce, few investigations have explored a key aspect of diversity among older workers: whether or not they consider themselves retired. Using a sample of workers ages 50 and older from the National Study of the Changing Workforce (2008), we apply career development theory and the job demand–control(–support) framework to investigate potential differences between working retirees (i.e. employed older adults 50+ who consider themselves retired) and working non-retirees (i.e. employed older adults 50+ who do not consider themselves retired) in terms of their job characteristics (i.e. demands, control, support) and how these job characteristics are related to job satisfaction. We find that working retirees report lower job demands and higher social support, and that there is limited evidence for the buffering hypothesis. Implications for researchers and employers are discussed.
The Bidirectional Relationship between Tuberculosis and Diabetes

The burden of tuberculosis (TB) especially in developing countries continues to remain high despite efforts to improve preventive strategies. Known traditional risk factors for TB include poverty, malnutrition, overcrowding, and HIV/AIDS; however, diabetes, which causes immunosuppression, is increasingly being recognized as an independent risk factor for tuberculosis, and the two often coexist and impact each other. Diabetes may also lead to severe disease, reactivation of dormant tuberculosis foci, and poor treatment outcomes. Tuberculosis as a disease entity on the other hand and some commonly used antituberculous medications separately may cause impaired glucose tolerance. This review seeks to highlight the impact of comorbid TB and diabetes on each other. It is our hope that this review will increase the awareness of clinicians and managers of TB and diabetes programs on the effect of the interaction between these two disease entities and how to better screen and manage patients.
Administrative Structure in Times of Changes: The Development of Estonian Ministries and Government Agencies 1990–2010

The article addresses the change in administrative structure at the center of the Estonian government during the twenty years of post-communist development. The focus is on three issues of theoretical relevance—the rate of change in the core parts of public administration, the aspired retrenchment of administrative structures, and the combination of national and international forces behind structural change. In analyzing the factors behind Estonian administrative formation, the initial deinstitutionalization of the politico-administrative system appears to be a critical factor for understanding the direction and content of the reforms undertaken.
Social Media and Productivity in the Workplace: Challenges and Constraints

The rise of social media is rapidly changing how organizations operate and communicate. Organizations of all kinds are looking for ways to seize advantage in this emerging era marked by greater immediacy, interactivity and transparency. The new media is growing so fast that it makes it imperative for employees to embrace the medium in the workplace. The aim of this conceptual paper is to examine the relevance of collaborative technology such as social media to employee productivity and discuss the significance, challenges and constraints of social media in the workplace. Based on previous studies, it was found that the use of social media has a positive impact on employee productivity, two-way communication and effective collaboration. Nonetheless, several other studies found the opposite as it was somewhat difficult to make direct correlation between productivity and social media. Thus, organizations should establish appropriate policies at workplace and determine how much use will be made of social media sites for job purposes. In general, organizations should work with, not against social media because organizations that fight the advancing technology are combating a losing battle.
Molecular paleobiological insights into the origin of the Brachiopoda

Most studies of brachiopod evolution have been based on their extensive fossil record, but molecular techniques, due to their independence from the rock record, can offer new insights into the evolution of a clade. Previous molecular phylogenetic hypotheses of brachiopod interrelationships place phoronids within the brachiopods as the sister group to the inarticulates, whereas morphological considerations suggest that Brachiopoda is a monophyletic group. Here, these hypotheses were tested with a molecular phylogenetic analysis of seven nuclear housekeeping genes combined with three ribosomal genes. The combined analysis finds brachiopods to be monophyletic, but with relatively weak support, and the craniid as the sister taxon of all other brachiopods. Phylogenetic‐signal dissection suggests that the weak support is caused by the instability of the craniid, which is attracted to the phoronids. Analysis of slowly evolving sites results in a robustly supported monophyletic Brachiopoda and Inarticulata (Linguliformea+Craniiformea), which is regarded as the most likely topology for brachiopod interrelationships. The monophyly of Brachiopoda was further tested with microRNA‐based phylogenetics, which are small, noncoding RNA genes whose presence and absence can be used to infer phylogenetic relationships. Two novel microRNAs were characterized supporting the monophyly of brachiopods. Congruence of the traditional molecular phylogenetic analysis, microRNAs, and morphological cladograms suggest that Brachiopoda is monophyletic with Phoronida as its likely sister group. Molecular clock analysis suggests that extant phoronids have a Paleozoic divergence despite their conservative morphology, and that the early brachiopod fossil record is robust, and is not affected by taphonomic factors relating to the late‐Precambrian/early‐Cambrian phosphogenic event.
Managing Athletic Department Touch Points: A Case Study of One Institution Using Importance-Performance Analysis

Athlete recruitment and delivery of the sport experience are critical components in determining the success of intercollegiate athletic teams and programs. Here, the athletic department brand and the associations of the brand achieved through “touch points” influence student-athletes’ perceptions of the athletic department. The purpose of this study therefore was to understand the perceptions held by student-athletes about the brand of the athletic department. Importance-Performance Analysis (IPA) and brand touch point theory were used to accomplish the study’s objective. Specifically, the authors analyzed surveys from 149 student-athletes based at one university in Ontario, Canada to consider athletic department “touch points. ” The results proved beneficial for highlighting areas of discrepancy between deemed importance and performance on key recruitment and delivery attributes including scholarship support, spectator support, special treatment, recognition, and quality of facilities.
Signaling Games and Stable Equilibria

Games in which one party conveys private information to a second through messages typically admit large numbers of sequential equilibria, as the second party may entertain a wealth of beliefs in response to out-of-equilibrium messages. By restricting those out-of-equilibrium beliefs, one can sometimes eliminate many unintuitive equilibria. We present a number of formal restrictions of this sort, investigate their behavior in specific examples, and relate these restrictions to Kohlberg and Mertens' notion of stability.
The effect of molecular weights of microencapsulating polymers on viability of mouse-cloned pancreatic β-cells: biomaterials, osmotic forces and potential applications in diabetes treatment

Abstract Introduction: Ideal cell-containing microcapsules should be capable of maintaining cell viability and exhibit significant structural stability to support cellular functionality. To date, such microcapsules remain unavailable; thus, this study used our well-established microencapsulating methods to examine a total of 32 different microencapsulating formulations and correlate polymers’ molecular weights (Mwt) and UDCA addition, with cell viability and microcapsules’ stability, postmicroencapsulation. Methods: MIN6 mouse-cloned pancreatic β-cells were microencapsulated using control (n = 16; without UDCA) and test (n = 16; with UDCA) different polymers. Confocal microscopic imaging, cell viability, and microcapsules’ stability were assessed. Results: Best cell viability (>50%) was obtained at average Mwt of 50,000 g/mol (poly-l-ornithine), followed by 110,000 g/mol (poly-l-lysine). There was no linear correlation between Mwt and viability. Confocal imagining showed similar microcapsules’ shape and cell distribution among all different polymers’ molecular weights, which suggests that the microencapsulating method was efficient and maintained microcapsules’ uniformity. UDCA addition resulted in enhanced osmotic stability of the microcapsules and improved cell viability, when the formulation contained 1% polylornithine, 1% polyethylene glycol, 20% Eudragit® NM30D, 1% polytetrafluoroethylene, or 5% pentamethylcyclopentasiloxane. Conclusions: UDCA addition improved microenvironmental conditions within the microcapsules but this effect was largely dependent on the polymer systems used.
Information from dynamic length changes improves reliability of static ultrasound fascicle length measurements

Purpose Various strategies for improving reliability of fascicle identification on ultrasound images are used in practice, yet these strategies are untested for effectiveness. Studies suggest that the largest part of differences between fascicle lengths on one image are attributed to the error on the initial image. In this study, we compared reliability results between different strategies. Methods Static single-image recordings and image sequence recordings during passive ankle rotations of the medial gastrocnemius were collected. Images were tracked by three different raters. We compared results from uninformed fascicle identification (UFI) and results with information from dynamic length changes, or data-informed tracking (DIT). A second test compared tracking of image sequences of either fascicle shortening (initial-long condition) or fascicle lengthening (initial-short condition). Results Intra-class correlations (ICC) were higher for the DIT compared to the UFI, yet yielded similar standard error of measurement (SEM) values. Between the initial-long and initial-short conditions, similar ICC values, coefficients of multiple determination, mean squared errors, offset-corrected mean squared errors and fascicle length change values were found for the DIT, yet with higher SEM values and greater absolute fascicle length differences between raters on the first image in the initial-long condition and on the final image in the initial-short condition. Conclusions DIT improves reliability of fascicle length measurements, without lower SEM values. Fascicle length on the initial image has no effect on subsequent tracking results. Fascicles on ultrasound images should be identified by a single rater and care should be taken when comparing absolute fascicle lengths between studies.
MEASURING THE MEMORY PARAMETER ON SEVERAL TRANSFORMATIONS OF ASSET RETURNS

The issue in this paper is to measure the memory parameter in several transformations of historical data of asset returns in the UK (xt) by means of fractionally integrated techniques. We use both parametric and semiparametric methods, and the results show that the power transformations of the absolute values of the returns (i.e., |xt|θ, with θ
Annual influenza vaccination

Despite national and international recommendations, annual influenza vaccination uptake among health care providers (HCPs) remains sub-optimal. This study investigated the uptake, enablers, and barriers to annual influenza vaccination in medicine, nursing, and physiotherapy students at the University of Notre Dame Australia, Fremantle, using an online survey and semi-structured interviews. In 2013, uptake rate of influenza vaccination was 36.3% (95% CI = 31.8–40.8%). Employment as a HCP (OR 1.6, 95% CI 1.1–2.5), being a medical student (OR 2.5, 95% CI 1.2–5.1) and eligibility for government-funded vaccine (OR 7.1, 95% CI 2.7–18.6) were independently associated with increased uptake. Awareness, cost, and convenience were identified as key barriers to vaccination with interview data suggesting that raising awareness of the benefits of influenza vaccination, along with improving student HCPs’ access to affordable, convenient vaccination are likely to improve uptake. Responsibility to increase uptake should be shared between universities and student HCPs.
Retinal Structure and Gene Therapy Outcome in Retinoschisin-Deficient Mice Assessed by Spectral-Domain Optical Coherence Tomography

Purpose Spectral-domain optical coherence tomography (SD-OCT) was used to characterize the retinal phenotype, natural history, and treatment responses in a mouse model of X-linked retinoschisis (Rs1-KO) and to identify new structural markers of AAV8-mediated gene therapy outcome. Methods Optical coherence tomography scans were performed on wild-type and Rs1-KO mouse retinas between 1 and 12 months of age and on Rs1-KO mice after intravitreal injection of AAV8-scRS/IRBPhRS (AAV8-RS1). Cavities and photoreceptor outer nuclear layer (ONL) thickness were measured, and outer retina reflective band (ORRB) morphology was examined with age and after AAV8-RS1 treatment. Outer retina reflective band morphology was compared to immunohistochemical staining of the outer limiting membrane (OLM) and photoreceptor inner segment (IS) mitochondria and to electron microscopy (EM) images of IS. Results Retinal cavity size in Rs1-KO mice increased between 1 and 4 months and decreased thereafter, while ONL thickness declined steadily, comparable to previous histologic studies. Wild-type retina had four ORRBs. In Rs1-KO, ORRB1was fragmented from 1 month, but was normal after 8 months; ORRB2 and ORRB3 were merged at all ages. Outer retina reflective band morphology returned to normal after AAV-RS1 therapy, paralleling the recovery of the OLM and IS mitochondria as indicated by anti–β-catenin and anti-COX4 labeling, respectively, and EM. Conclusions Spectral-domain OCT is a sensitive, noninvasive tool to monitor subtle changes in retinal morphology, disease progression, and effects of therapies in mouse models. The ORRBs may be useful to assess the outcome of gene therapy in the treatment of X-linked retinoschisis patients.
Direct Amplification and Genotyping of Dientamoeba fragilis from Human Stool Specimens

ABSTRACT Dientamoeba fragilis is a globally occurring parasite that has been recognized as a causative agent of gastrointestinal symptoms. A single-round PCR was developed to detect D. fragilis DNA directly from human stool samples. The genetic diversity of D. fragilis from 93 patients and 6 asymptomatic carriers was examined by PCR followed by restriction fragment length polymorphism and sequencing of part of the small-subunit rRNA gene. The data show that D. fragilis sequences can be studied directly from fecal specimens despite the absence of a cyst stage and without the need for prior culturing. In addition, the results suggest strongly that D. fragilis shows remarkably little variation in its small-subunit rRNA gene.
Lenalidomide in combination with melphalan and dexamethasone in patients with newly diagnosed AL amyloidosis: a multicenter phase 1/2 dose-escalation study.

New treatment options are required for primary systemic amyloid light chain (AL) amyloidosis. This phase 1/2 dose-escalation study aimed to determine the maximum tolerated dose (MTD) of lenalidomide in combination with melphalan and dexamethasone (M-dex), and assess the efficacy and tolerability of this therapy for patients with de novo AL amyloidosis. Twenty-six patients were enrolled across 4 cohorts: M-dex + lenalidomide 5, 10, 15, and 20 mg once daily on days 1 to 21 in a 28-day cycle. No dose limiting toxicity (DLT) was observed in cohorts 1, 2, and 3. 4. Seven patients in cohort 4, M-dex + lenalidomide 20 mg/day, experienced DLT. MTD was defined as 15 mg of lenalidomide. A complete hematologic response was achieved in 42% at the dose of 15 mg of lenalidomide per day. After a median follow-up of 19 months, estimated 2-year overall survival (OS) and event-free survival (EFS) were 80.8% and 53.8%, respectively. Hematologic and organ responses were both associated with superior EFS rates (P = .0001). A higher EFS was also observed in patients whose free light chains decreased by more than 50% during therapy (P = .019). Lenalidomide 15 mg/d + M-dex is a new effective combination therapy in patients with newly diagnosed AL amyloidosis. This study is registered at www.clinicaltrials. gov as NCT00621400.
Forecasting Wheat Production in Pakistan

This study analyzes the future prospects of wheat production in Pakistan. Parameters of the forecasting model are obtained by estimating a Cobb-Douglas production function for wheat, while future values of various inputs are obtained as dynamic forecasts on the basis of separate ARIMA estimates for each input and for each province. Input forecasts and parameters of the wheat production function are then used to generate wheat forecasts. The results of the study show that the most important variables for predicting wheat production per hectare (in order of importance) are: lagged output, labor force, use of tractors, and sum of the rainfall in the months of November to March. The null hypotheses of common coefficients across provinces for most of the variables cannot be rejected, implying that all variables play the same role in wheat production in all the four provinces. Forecasting performance of the model based on out-of-sample forecasts for the period 2005-06 is highly satisfactory with 1.81% mean absolute error. The future forecasts for the period of 2007-15 show steady growth of 1.6%, indicating that Pakistan will face a slight shortage of wheat output in the future.
Therapeutic modification of nuclear factor kappa B binding activity and tumor necrosis factor-alpha gene expression during acute biliary pancreatitis.

The role of cytokines has been well documented in the pathogenesis of acute pancreatitis. Antibodies against specific cytokines have been used to treat pancreatitis, with mixed results. The transcription factor nuclear factor (NF)-kappa B is a pleiotropic regulator of many genes involved in stress and inflammatory responses. The aim of this study was to prevent the NF-kappa B binding activity and tumor necrosis factor (TNF)-alpha gene overexpression as a possible therapeutic intervention for acute pancreatitis. Reversible acute biliary pancreatitis was induced in male Sprague Dawley rats as established in this laboratory. The animals were sacrificed at 0, 5, 15, 30 min and 1, 2, 3, 4, 6, 8, 10, 12, and 24 hours after the induction of pancreatitis. NF-kappa B binding activity was determined by electrophoretic mobility shift assay, and TNF-alpha gene expression was assayed by reverse transcription-PCR. NF-kappa B binding activity was markedly higher around 4 hours and persisted up to 24 hours after pancreatitis induction in animals with acute pancreatitis, whereas TNF-alpha mRNA levels peaked at 24 hours. When amobarbital (to block NF-kappa B activation) was given (60 mg/kg body weight, I.P.) 3 hours before induction of pancreatitis, the activation of NF-kappa B and the overexpression of TNF-alpha gene was prevented, with significantly decreased severity of pancreatitis as assessed by amylase and clinical recovery. We conclude that 1) preventing the activation of NF-kappa B eliminates the induced overexpression of inflammatory cytokines (TNF-alpha) in acute pancreatitis, 2) such intervention correlates with clinical improvement in pancreatitis, and 3) this genetic modification offers a possible therapeutic intervention in acute pancreatitis.
Determinants of Internet Financial Reporting by New Zealand Companies

The development of the Internet as a global medium for the dissemination of corporate financial information creates a new reporting environment. Extensive literature examines the determinants of voluntary financial reporting through traditional media such as print-based annual reports. This paper extends this literature by examining the voluntary adoption of the Internet as a medium for transmitting financial reports and determinants of such voluntary practice by New Zealand companies. The results indicate that some determinants of traditional financial reporting - firm size, liquidity, industrial sector and spread of shareholding - are determinants of voluntary adoption of Internet financial reporting (IFR). However, other firm characteristics, such as leverage, profitability and internationalization do not explain the choice to use the Internet as a medium for corporate financial reporting.
Police Reporting Practices for Sexual Assault Cases in Which “The Victim Does Not Wish to Pursue Charges”

Prior research examining sexual assault case attrition has focused on the processing of cases across the justice system. Studies have examined arrest decision making and prosecutorial decision making in an attempt to better understand where and when cases drop out of the system. Less explored are police reporting practices during the initial stage of processing for cases in which the officer stated that the victim chose to drop her case. We addressed this gap in the literature by reviewing law enforcement incident reports at their onset, specifically; we examine reports of cases in which the officer reported the victim chose to drop the case. Results indicated that of the 125 cases of sexual assault reported to the police, 41 reports (32.8%) stated that the victim decided to no longer pursue charges. However, few police reports (30.2%) provided a clear rationale for why the victim decided to no longer pursue charges. Results of this study call for more standardized police reporting practices and point to the need for future research into the initial stage of law enforcement involvement in adult sexual assault cases.