Miracle-dz/UniFAR-FTUs huggingface dataset:
Early rearing history influences oxytocin receptor epigenetic regulation in rhesus macaques

Significance Epigenetically programmed stress adaptation may be a conduit for informing offspring of environmental challenge. We employed ChIP-sequencing to examine effects of early environment on epigenetic regulation using hippocampal samples from macaques exposed to disruption in maternal care. We found decreased H3K4me3 binding at genes critical to behavioral stress response, the most robust being the oxytocin receptor gene (OXTR), for which we observed a corresponding decrease in RNA expression. Post hoc analysis showed that a gain-of-function OXTR SNP rescued behavioral differences in early stress-exposed subjects. Our data suggest that epigenetic down-modulation of OXTR in brain could contribute to behavioral differences observed in early stress-exposed subjects and that functional genetic variation plays a role. These could have translational implications for human psychiatric disease and personality disorders. Adaptations to stress can occur through epigenetic processes and may be a conduit for informing offspring of environmental challenge. We employed ChIP-sequencing for H3K4me3 to examine effects of early maternal deprivation (peer-rearing, PR) in archived rhesus macaque hippocampal samples (male, n = 13). Focusing on genes with roles in stress response and behavior, we assessed the effects of rearing on H3K4me3 binding by ANOVA. We found decreased H3K4me3 binding at genes critical to behavioral stress response, the most robust being the oxytocin receptor gene OXTR, for which we observed a corresponding decrease in RNA expression. Based on this finding, we performed behavioral analyses to determine whether a gain-of-function nonsynonymous OXTR SNP interacted with early stress to influence relevant behavioral stress reactivity phenotypes (n = 194), revealing that this SNP partially rescued the PR phenotype. PR infants exhibited higher levels of separation anxiety and arousal in response to social separation, but infants carrying the alternative OXTR allele did not exhibit as great a separation response. These data indicate that the oxytocin system is involved in social-separation response and suggest that epigenetic down-modulation of OXTR could contribute to behavioral differences observed in PR animals. Epigenetic changes at OXTR may represent predictive adaptive responses that could impart readiness to respond to environmental challenge or maintain proximity to a caregiver but also contribute to behavioral pathology. Our data also demonstrate that OXTR polymorphism can permit animals to partially overcome the detrimental effects of early maternal deprivation, which could have translational implications for human psychiatric disorders.
Axonal projections of pulmonary slowly adapting receptor relay neurons in the rat

We elucidated efferent projections of second‐order relay neurons (P‐cells) activated by afferents originating from slowly adapting pulmonary receptors (SARs) to determine the central pathway of the SAR‐evoked reflexes. Special attention was paid to visualizing the P‐cell projections within the nucleus tractus solitarii (NTS), which may correspond to the inhibitory pathway from P‐cells to second‐order relay neurons (RAR‐cells) of rapidly adapting pulmonary receptors. P‐cells were recorded from the NTS in Nembutal‐anesthetized, paralyzed, and artificially ventilated rats. First, we used electrophysiological methods of antidromic mapping and showed that the majority of the P‐cells examined projected their axons to the caudal NTS and to the dorsolateral pons corresponding to the parabrachial complex. Second, a mixture of HRP and Neurobiotin was injected intracellularly or juxtramembranously into P‐cells. (1) Stained P‐cells (n = 7) were located laterally to the solitary tract and had dendrites extending characteristically along the lateral border of the solitary tract. (2) All P‐cells had stem axons projecting to the ipsilateral medulla. Of these, the axons from five P‐cells projected to the nucleus ambiguus and its vicinity with distributing boutons. Some of these axons further ascended in the ventrolateral medulla, and distributed boutons in the areas ventral or ventrolateral to the nucleus ambiguus. (3) All the P‐cells had axonal branches with boutons in the NTS area. In particular, axons from three P‐cells projected bilaterally to the medial NTS caudal to the obex, i.e., to the area of RAR‐cells. These results show anatomic substrates for the connections implicated in the P‐cell inhibition of RAR‐cells as well as the SAR‐induced respiratory reflexes. J. Comp. Neurol. 446:81–94, 2002. © 2002 Wiley‐Liss, Inc.
Differentiation of pathogenic from nonpathogenic Entamoeba histolytica by restriction fragment analysis of a single gene amplified in vitro

We previously reported the identification of homologous cDNA clones derived from a pathogenic isolate and a nonpathogenic isolate of Entamoeba histolytica, which had been designated cEh-P1 and cEh-NP1, respectively. Sequence analysis of both clones had revealed 10% nucleic acid substitutions, which were dispersed over the entire sequence. This genetic difference had been found to be conserved between all four pathogenic and all five nonpathogenic laboratory strains of E. histolytica tested. On the basis of nucleic acid substitutions, we have now developed a sensitive assay to distinguish pathogenic from nonpathogenic forms of E. histolytica by using fresh clinical isolates. Comparing the sequence of cEh-P1 and cEh-NP1, we identified a 482-bp segment that contained identical 5' and 3' ends but differed in internal cleavage sites for restriction endonucleases. By using oligonucleotide primers corresponding to the 5' and 3' ends of this segment, the corresponding gene was amplified by the polymerase chain reaction. Endonuclease digestion of the amplified DNA yielded restriction fragments that are characteristic for pathogenic and nonpathogenic forms. This assay allows the detection and classification of fewer than 10 amoebae within a few hours. The differentiation of 48 isolates into pathogenic and nonpathogenic strains by using this method corresponded to the clinical status of the infected individuals and to the classification obtained by isoenzyme determination. The results further support the concept that pathogenic and nonpathogenic strains of E. histolytica constitute distinct subspecies.
Public Opinion on National Exam Policies in Indonesia

Abstract Every new policy by Indonesian government in National Examination (NE) implementation always obtains different respond from public. Since the implementation, NE system already experienced many changes, but in recent years this system receives serious critiques. As a result, government then abolished this system as graduation determinant in 2014. This research analyzes public opinion, in the form of positive and negative sentiment toward NE policy, and factors that drive the opinions. Data in this research obtained from online news media from 2012 to 2015. The result shows that public sentiment fluctuating from year to year and depends on three important factors, i.e. political pressure, extreme events, and media coverage.
Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi‐guided multiplexed metabolic tuning

The application of rational design in reallocating metabolic flux to overproduce desired chemicals is always restricted by the native regulatory network. Here, we demonstrated that in vitro modular pathway optimization combined with in vivo multiplexed combinatorial engineering enables effective characterization of the bottleneck of a complex biosynthetic cascade and improves the output of the engineered pathway. As a proof of concept, we systematically identified the rate‐limiting step of a five‐gene malate biosynthetic pathway by combinatorially tuning the enzyme loads of a reconstituted biocatalytic reaction in a cell‐free system. Using multiplexed CRISPR interference, we subsequently eliminated the metabolic constraints by rationally assigning an optimal gene expression pattern for each pathway module. The present engineered strain Escherichia coli B0013‐47 exhibited a 2.3‐fold increase in malate titer compared with that of the parental strain, with a yield of 0.85 mol/mol glucose in shake‐flask culture and titer of 269 mM (36 g/L) in fed‐batch cultivation. The strategy reported herein represents a powerful method for improving the efficiency of multi‐gene pathways and advancing the success of metabolic engineering.
Second Life (SL) in Education: The Intensions to Use at University of Bahrain

Second Life (SL) is an online virtual world that is capturing popularity in academic institutions as an alternative means for collaborative and distance education. University of Bahrain is an academic institution with an intension to apply this application to overcome some of the obstacles they are encountering in education. Before using SL in education in the academic institutions, it is essential to measure the students' initial experience and the factors associated with the intension to use it to enforce its success. Therefore, this study is to present the experience of using SL at University of Bahrain in terms of the students' initial experience and factors that affect their intention to use it. Toward achieving the objectives a survey was employed using Technology Acceptance Model (TAM) and extended factors are employed for this purpose. The model is tested through a survey administered to UOB's students. Results of the initial investigation suggest that that almost two third of the respondents agreed on SL being easy to use and useful tool in education thus accepting the use of it for educational purposes. Results of the research show that perceived ease of use affects user's intention to adopt SL through perceived usefulness. Computer self-efficacy, computer playfulness, and computer anxiety are also significant antecedents to perceived ease of use of virtual worlds. Implications for educators and designers are presented.
Coordinate regulation of canine glomeruli and adrenal angiotensin receptors by dietary sodium manipulation.

BACKGROUND This study evaluated the effects of dietary sodium manipulation in dogs on the regulation of canine angiotensin receptors (cAT1 and cAT2) in the kidney and adrenal. METHODS Isolated glomeruli and membranes from renal medulla and the adrenal gland were used in radioligand binding assays from two groups of dogs: dogs maintained on low-sodium diet for two weeks followed by a high-sodium diet for two weeks (H), and dogs were maintained on the reverse schedule (L). RESULTS Analysis of the binding data showed that dietary sodium manipulation had no significant effects on cAT1 and cAT2 receptor binding affinities in glomeruli, renal medulla, and adrenal tissues. In contrast, dietary sodium loading induced a marked increase in cAT1 receptor expression in both the glomeruli and adrenal compared with receptor expression in salt-restricted animals [H/L ratio: glomeruli (1.5), renal medulla (1.1), adrenal (1.6)] that inversely correlated with the activity of the plasma renin angiotensin system. Conversely, adrenal cAT2 receptor expression was regulated in an inverse manner in the H and L animal groups [H/L ratio: 0.7]. CONCLUSIONS This study demonstrates that renal glomerular and adrenal AT1 receptors in the dog are coordinately down-regulated by dietary sodium restriction compared with sodium loading, which is distinctly different from the reciprocal regulation observed for rat AT1 receptors in these tissues. Collectively, these data suggest that postreceptor events in dogs are determinants of the aldosterone response observed during sodium restriction. These findings have important implications for the regulation of the renin-angiotensin system in humans, and suggest that coordinate regulation of AT1 receptors in the adrenal and glomeruli represent a negative feedback mechanism that when functioning normally prevents fluctuations of arterial blood pressure and development of arterial hypertension in response to changes in dietary sodium.
A feasibility study to determine the benefits of upper extremity virtual rehabilitation therapy for coping with chronic pain post-cancer surgery

Background: Persistent pain in shoulder and arm following post-surgical breast cancer treatment can lead to cognitive and physical deficits. Depression is also common in breast cancer survivors. Virtual reality therapy with integrative cognitive and physical rehabilitation has not been clinically trialed for this population. The novel BrightArm Duo technology improved cognition and upper extremity (UE) function for other diagnoses and has great potential to benefit individuals coping with post-surgical breast cancer pain. Objectives: The aim of this study was to explore the feasibility of BrightArm Duo therapy for coping with post-surgical chronic pain and associated disability in breast cancer survivors with depression. Methods: BrightArm Duo is a robotic rehabilitation table modulating gravity loading on supported forearms. It tracks arm position and grasping strength while patients play three-dimensional (3D) custom integrative rehabilitation games. Community-dwelling women (N = 6) with post-surgical breast cancer pain in the upper arm trained on the system twice a week for 8 weeks. Training difficulty increased progressively in game complexity, table tilt and session length (20–50 minutes). Standardized assessments were performed before and after therapy for pain, cognition, emotion, UE function and activities of daily living. Results: Subjects averaged upwards of 1300 arm repetitions and 850 hand grasps per session. Pain intensity showed a 20% downward trend (p = 0.1) that was corroborated by therapist observations and participant feedback. A total of 10 out of 11 cognitive metrics improved post-training (p = 0.01) with a significant 8.3-point reduction in depression severity (p = 0.04). A total of 17 of 18 range of motion metrics increased (p < 0.01), with five affected-side shoulder improvements above the Minimal Clinically Important Difference (8°). In all, 13 out of 15 strength and function metrics improved (p = 0.02) with lateral deltoid strength increasing 7.4 N on the affected side (p = 0.05). Conclusion: This pilot study demonstrated feasibility of using the BrightArm Duo Rehabilitation System to treat cancer survivors coping with upper body chronic pain. Outcomes indicate improvement in cognition, shoulder range, strength, function and depression.
Normative uncertainty and middle-status innovation in the US daily newspaper industry

This article focuses on normatively uncertain innovations and asks when and how organizational status affects the adoption and implementation of these innovations. I argue that middle-status organizations perceive normative uncertainty more as an opportunity for gain, whereas high- and low-status organizations perceive it more as a threat of loss and competition. Consequently, middle-status organizations are likely to be the first to adopt normatively uncertain innovations and to implement them in a way that emphasizes normative uncertainty. Event history and negative binomial regression analyses of the US newspaper industry from 1993 to 2007, the period after the emergence of digital media that was normatively uncertain, support my theoretical arguments. Middle-status newspapers launched their websites faster than other newspapers did. In addition, they emphasized interactivity on the web, which could potentially change the identity of newspapers from sole news producers to facilitators.
Financial innovation and monetary policy transmission mechanism in Pakistan

In the recent past there are remarkable financial innovations in Pakistan which have the implications for the monetary policy. In Pakistan there is no or little empirical evidence on the impact of financial innovation on monetary policy transmission mechanism. In this paper we fill this gap by analyzing the impact of financial innovation on monetary policy transmission mechanism by using the interest rate channel. We use the quarterly date covering the period, 1981Q1 to 2010Q4 for Pakistan and for estimation we use OLS. We found that the interest rate channel of monetary policy transmission mechanism dampens by the interest rate channel.
Genetic-Fuzzy Data Envelopment Analysis Model for Evaluating Financial Institutions Relative Productivity in a Fluctuating Economic Market

This paper presents a Genetic Algorithm Fuzzy Data Envelopment Analysis (GA-FDEA) model that caters for optimal selecting of economic indicators for the measurement of relative productivity and performance of financial institutions. Imprecise or uncertain data of financial institutions due to varying monetary policies and market risk were retrieved from Nigeria Stock Exchange Commission and evaluated. It was observed that GA-FDEA provides better results than the conventional DEA. The findings provide economic barometers for ascertaining the viability of these institutions toward bringing the expected growth of these institutions and the nation at large.
Center for Economic Institutions

Using new evidence from servant contracts, 1600-1890, we estimate women’s wages in Japan. Women’s wages could only sustain 1.5-2 people up to 1900, the lowest recorded in the pre-industrial world. We then show the gender wage ratio was 0.7, higher than in Western Europe. Despite this, Japan had lower female empowerment for two reasons. First, absolute wages were low, so women were not economically autonomous. Second, landownership incomes were mostly earned by men, raising their bargaining positions. Low female empowerment in Japan could also explain the early and universal marriage of its women unlike their empowered Western European coun-
Automatic musical genre classification using sparsity-eager support vector machines

Constructing robust categorical and typological classifiers, i.e., finding auditory constructs utilized for describing music categories, is an important problem in music genre classification. Supervised methods such as support vector machine (SVM) achieve state of the art performance for genre classification but suffer from over-fitting on training examples. In this paper, we introduce a supervised classifier, ℓ1-SVM, that utilizes sparse methods to deal with over-fitting for genre classification. We compare the proposed algorithm to competing learning methods such as SVM, logistic regression, and ℓ1-regression for genre classification. Experimental results suggest that the proposed method using short-time audio features (MFCCs) outperforms the baseline algorithms in terms of the average classification accuracy rate of musical genres.
Intracellular pH Changes During Neutrophil Activation: Na+ /H+ Antiport

Activation of the Na+ /H+ antiport mechanism was studied in human neutrophils by monitoring intracellular pH with a carboxyfluorescein derivative. N‐formyl‐methionylleucyl‐phenylalanine (FMLP) and phospholipase C (PLC) induced biphasic pH changes. Amiloride, which inhibits the antiport, completely blocked alkalinization but enhanced acidification. Polymyxin B, which inhibits protein kinase C, only blocked alkalinization. Activation with phorbol 12‐myristate 13‐acetate (PMA) led to alkalinization only; this was inhibited by amiloride or polymyxin B. Thus, during polymorphonuclear leukocyte (PMN) activation, Intracellular alkalinization appears to be mediated by an amiloride‐sensitive Na+ /H+ antiport. Antiport activity can also be blocked indirectly by inhibition of protein kinase C activity. Early intracellular acidification does not appear to require kinase activity but is observed when phospholipids are remodeled with PLC. The antiport was also activatable by hypertonic buffered media. This response did not appear to be mediated by protein kinase C because it was unaffected by polymyxin B. Finally, superoxide generation was investigated. It is affected by, but not soley controlled by, either antiport or protein kinase C activity.
Development of Large-scale Cross-linking Mass Spectrometry*

Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level. Specifically, there is an unmet need for comprehensive software that can reliably identify cross-linked peptides from large data sets. In this review we provide supporting information to reason that targeted proteomics of cross-links may provide the required sensitivity to reliably detect and quantify cross-linked peptides and that a reporter ion signature for cross-linked peptides may become a useful approach to increase confidence in the identification process of cross-linked peptides. In addition, the review summarizes the recent advances in CLMS workflows using the analysis of condensin complex in intact chromosomes as a model complex.
Pricing and calibration with stochastic local volatility models in a monte carlo setting

A general purpose of mathematical models is to accurately mimic some observed phenomena in the real world. In financial engineering, for example, one aim is to reproduce market prices of financial contracts with the help of applied mathematics. In the Foreign Exchange (FX) market, the so-called implied volatility smile plays a key role in the pricing and hedging of financial derivative contracts. This volatility smile is a phenomenon that reflects the prices of European-type options for different strike prices; the implied volatility tends to be higher for options that are deeper In The Money and Out of The Money than options that are approximately At The Money. In order for a pricing model to be accepted in the financial industry, it should at least be able to accurately price back the most simple financial derivative contracts, namely European call and put options. In other words, the model should calibrate well to the implied volatility smile observed in the financial market. The calibration should not only be accurate, but also reasonably fast. Another feature we wish the financial asset model to possess, is an accurate pricing of so-called exotic financial products. Exotic products are not traded on regular exchanges, but over-the-counter, i.e. directly between two parties without the supervision of an exchange. An example is a barrier option, which is a financial contract of which its payoff depends on the possible event that the underlying asset price hits a certain pre-determined level. The model prices of these path-dependent contracts are determined by the transition densities of the relevant underlying asset(s) between future time-points. These transition densities are reflected by the forward volatility smile the model implies; in order for the model to accurately price exotic products, it should yield realistic forward volatilities.