Miracle-dz/UniFAR-FTUs huggingface dataset:
An Association Analysis between Mitochondrial DNA A10398G Polymorphism and Temperament in Japanese Young Adults

The mitochondrial (mt) DNA C5178A and A10398G polymorphisms have been reported to be associated with mental disorders such as bipolar disorder. However, the effects of these polymorphisms on temperament in healthy people are poorly understood. Evaluating healthy subjects can have the advantage of providing new strategies for maintaining psychological health and preventing mental illness. We examined the association between mtDNA polymorphisms and temperament in Japanese students. There was no significant difference in examined temperament when analysed by genotypes, 5178–10398 haplotypes, or sex. The subgroup analysis based on sex indicated that there was an interactive effect of the mtDNA A10398G polymorphism and sex on anxiety and obsession. This finding is preliminary and cannot exclude the possibility of false-positive due to small sample size (144 subjects) and multiple statistical testing. Further studies involving a larger sample size or other ethnic groups are necessary to confirm that mtDNA A10398G polymorphism can be a genetic factor for temperament.
On the Redundancy of Slepian–Wolf Coding

In this paper, the redundancy of both variable and fixed rate Slepian-Wolf coding is considered. Given any jointly memoryless source-side information pair {(Xi, Yi)}<sub>i=1</sub> <sup>infin</sup> with finite alphabet, the redundancy R<sup>n</sup>(isin<sub>n</sub>) of variable rate Slepian-Wolf coding of X<sub>1</sub> <sup>n</sup> with decoder only side information Y<sub>1</sub> <sup>n</sup> depends on both the block length n and the decoding block error probability isin<sub>n</sub>, and is defined as the difference between the minimum average compression rate of order n variable rate Slepian-Wolf codes having the decoding block error probability less than or equal to isin<sub>n</sub>, and the conditional entropy H(X|Y), where H(X|Y) is the conditional entropy rate of the source given the side information. The redundancy of fixed rate Slepian-Wolf coding of X<sub>1</sub> <sup>n</sup> with decoder only side information Y<sub>1</sub> <sup>n</sup> is defined similarly and denoted by R<sub>F</sub> <sup>n</sup>(isin<sub>n</sub>). It is proved that under mild assumptions about isin<sub>n</sub>, R<sup>n</sup>(isin<sub>n</sub>) = d<sub>v</sub>radic-log isin<sub>n</sub>/n + (oradic-log isin<sub>n</sub>/n) and R<sub>F</sub> <sup>n</sup>(isin<sub>n</sub>) - d<sub>f</sub>radic-log isin<sub>n</sub>/n + o(radic-log isin<sub>n</sub>/n), where df and dnu are two constants completely determined by the joint distribution of the source-side information pair. Since d<sub>v</sub> is generally smaller than d<sub>f</sub>, our results show that variable rate Slepian-Wolf coding is indeed more efficient than fixed rate Slepian-Wolf coding.
High rates of behavioral problems in perinatally HIV-infected children are not linked to HIV disease.

OBJECTIVE Descriptive studies and clinical reports have suggested that human immunodeficiency virus (HIV)-positive children are at risk for behavioral problems. Inadequate control groups and sample sizes have limited the ability of investigators to consider multiple influences that place HIV-positive children at risk for poor behavioral outcomes. We examined the unique and combined influences of HIV, prenatal drug exposure, and environmental factors on behavior in children who were perinatally exposed to HIV. METHODS Participants included 307 children who were born to HIV-positive mothers (96 HIV infected and 211 seroreverters) and enrolled in a natural history, longitudinal study of women to infant HIV transmission. Caregivers completed parent behavioral rating scales, beginning when the children were 3 years old. Data were also collected on prenatal drug exposure; child age, gender, and ethnicity; caregiver relationship to child; and birth complications. RESULTS Multivariate analyses comparing the HIV-infected children with perinatally exposed but uninfected children from similar backgrounds failed to find an association between either HIV status or prenatal drug exposure and poor behavioral outcomes. The strongest correlates of increased behavioral symptoms were demographic characteristics. CONCLUSIONS This study suggests that although a high prevalence of behavioral problems does exist among HIV-infected children, neither HIV infection nor prenatal drug exposure is the underlying cause. Rather, other biological and environmental factors are likely contributors toward poor behavioral outcomes.
ANALISIS KOMPARASI USAHATANI KELAPA SAWIT SWADAYA MENURUT TIPOLOGI LAHAN DI KABUPATEN INDRAGIRI HILIR

Farmers income palm patterns of independent smallholders in Indragiri Hilir Distric were low, presumably because differences of land typology. There are four typologies of land in Indragiri Hilir, namely mainland land, peat tidal, peat marine and marine. This study aims to determine the farmers palm income based typology of land. The quantitative analysis is done by building a model of multiple linear regression analysis with dummy variables. This research show that farmers income palm patterns of independent smallholders in the Indragiri Hilir District on the mainland land typology is the best compared to the typology of peat tidal, peat marine and marine. The highest net income is on the mainland soil typology, typology further peatland tidal and coastal lands.
Histone Demethylase UTX and Chromatin Remodeler BRM Bind Directly to CBP and Modulate Acetylation of Histone H3 Lysine 27

ABSTRACT Trithorax group (TrxG) proteins antagonize Polycomb silencing and are required for maintenance of transcriptionally active states. We previously showed that the Drosophila melanogaster acetyltransferase CREB-binding protein (CBP) acetylates histone H3 lysine 27 (H3K27ac), thereby directly blocking its trimethylation (H3K27me3) by Polycomb repressive complex 2 (PRC2) in Polycomb target genes. Here, we show that H3K27ac levels also depend on other TrxG proteins, including the histone H3K27-specific demethylase UTX and the chromatin-remodeling ATPase Brahma (BRM). We show that UTX and BRM are physically associated with CBP in vivo and that UTX, BRM, and CBP colocalize genome-wide on Polycomb response elements (PREs) and on many active Polycomb target genes marked by H3K27ac. UTX and BRM bind directly to conserved zinc fingers of CBP, suggesting that their individual activities are functionally coupled in vivo. The bromodomain-containing C terminus of BRM binds to the CBP PHD finger, enhances PHD binding to histone H3, and enhances in vitro acetylation of H3K27 by recombinant CBP. brm mutations and knockdown of UTX by RNA interference (RNAi) reduce H3K27ac levels and increase H3K27me3 levels. We propose that direct binding of UTX and BRM to CBP and their modulation of H3K27ac play an important role in antagonizing Polycomb silencing.
Easily Identifiable Discourse Relations

We present a corpus study of local discourse relations based on the Penn Discourse Tree Bank, a large manually annotated corpus of explicitly or implicitly realized relations. We show that while there is a large degree of ambiguity in temporal explicit discourse connectives, overall connectives are mostly unambiguous and allow high-accuracy prediction of discourse relation type. We achieve 93.09% accuracy in classifying the explicit relations and 74.74% accuracy overall. In addition, we show that some pairs of relations occur together in text more often than expected by chance. This finding suggests that global sequence classification of the relations in text can lead to better results, especially for implicit relations.
The Optimal Allocation of Prizes in Contests

We study a contest with multiple (not necessarily equal) prizes. Contestants have private information about an ability parameter that affects their costs of bidding. The contestant with the highest bid wins the first prize, the contestant with the second-highest bid wins the second prize, and so on until all the prizes are allocated. All contestants incur their respective costs of bidding. The contest's designer maximizes the expected sum of bids. Our main results are: 1) We display bidding equlibria for any number of contestants having linear, convex or concave cost functions, and for any distribution of abilities. 2) If the cost functions are linear or concave, then, no matter what the distribution of abilities is, it is optimal for the designer to allocate the entire prize sum to a single ''first'' prize. 3) We give a necessary and sufficient conditions ensuring that several prizes are optimal if contestants have a convex cost function.
Combinatorial modification of multiple lignin traits in trees through multigene cotransformation

Lignin quantity and reactivity [which is associated with its syringyl/guaiacyl (S/G) constituent ratio] are two major barriers to wood-pulp production. To verify our contention that these traits are regulated by distinct monolignol biosynthesis genes, encoding 4-coumarate–CoA ligase (4CL) and coniferaldehyde 5-hydroxylase (CAld5H), we used Agrobacterium to cotransfer antisense 4CL and sense CAld5H genes into aspen (Populus tremuloides). Trees expressing each one and both of the transgenes were produced with high efficiency. Lignin reduction by as much as 40% with 14% cellulose augmentation was achieved in antisense 4CL plants; S/G-ratio increases as much as 3-fold were observed without lignin quantity change in sense CAld5H plants. Consistent with our contention, these effects were independent but additive, with plants expressing both transgenes having up to 52% less lignin, a 64% higher S/G ratio, and 30% more cellulose. An S/G-ratio increase also accelerated cell maturation in stem secondary xylem, pointing to a role for syringyl lignin moieties in coordinating xylem secondary wall biosynthesis. The results suggest that this multigene cotransfer system should be broadly useful for plant genetic engineering and functional genomics.
Secure and Efficient Data Transmission for Cluster-Based Wireless Sensor Networks

Secure data transmission is a critical issue for wireless sensor networks (WSNs). Clustering is an effective and practical way to enhance the system performance of WSNs. In this paper, we study a secure data transmission for cluster-based WSNs (CWSNs), where the clusters are formed dynamically and periodically. We propose two secure and efficient data transmission (SET) protocols for CWSNs, called SET-IBS and SET-IBOOS, by using the identity-based digital signature (IBS) scheme and the identity-based online/offline digital signature (IBOOS) scheme, respectively. In SET-IBS, security relies on the hardness of the Diffie-Hellman problem in the pairing domain. SET-IBOOS further reduces the computational overhead for protocol security, which is crucial for WSNs, while its security relies on the hardness of the discrete logarithm problem. We show the feasibility of the SET-IBS and SET-IBOOS protocols with respect to the security requirements and security analysis against various attacks. The calculations and simulations are provided to illustrate the efficiency of the proposed protocols. The results show that the proposed protocols have better performance than the existing secure protocols for CWSNs, in terms of security overhead and energy consumption.
The Influence of Knowledge, Motivation, and Attitude Toward The Behavior of Housewife to Eradicate of Aedes Aegepty Mosquito Nest (PSN)

Semarang city is the region with the highest dengue hemorrhagic fever cases in central java province. Eradication of aedes aegepty mosquito nest is one of the efforts considered appropriate in the prevention and eradication of dengue hemorrhagic fever. The active participation of housewives is necessary, the participation of housewives depends on the knowledge, motivation, and attitudes of the community towards the disease and its prevention. The purpose of this research is to analyze the influence of knowledge, motivation, and attitude toward the behavior of housewife to eradicate aedes aegepty mosquito nest (PSN). This research methos is quantitative with cross sectional design.Population of all housewives in Bulustalan Village Semarang, the sample amounted to 90 samples using purposive sampling technique. The results showed that there was an influence between knowledge on the behavior of mosquito nest eradication (p = 0,000). There is an influence between motivation to the behavior of mosquito nest eradication value (p = 0.012). There is an influence between attitudes toward the behavior of mosquito nest eradication value (p = 0.000). Logistic regression results showed that the more dominant knowledge influenced the behavior of mosquito nest eradication (p = 0,008) and Exp (B) value 4,365. The conclusion of housewife who has knowledge, motivation, and good attitude affect the behavior of housewife to eradicate aedes aegepty mosquito nest (PSN)
Unrewarded Object Combinations in Captive Parrots

In primates, complex object combinations during play are often regarded as precursors of functional behavior. Here we investigate combinatory behaviors during unrewarded object manipulation in seven parrot species, including kea, African grey parrots and Goffin cockatoos, three species previously used as model species for technical problem solving. We further examine a habitually tool using species, the black palm cockatoo. Moreover, we incorporate three neotropical species, the yellow- and the black-billed Amazon and the burrowing parakeet. Paralleling previous studies on primates and corvids, free object-object combinations and complex object-substrate combinations such as inserting objects into tubes/holes or stacking rings onto poles prevailed in the species previously linked to advanced physical cognition and tool use. In addition, free object-object combinations were intrinsically structured in Goffin cockatoos and in kea.
Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner

Significance Although implicated, the role of herpes simplex virus (HSV) infected cell culture polypeptide 27 (ICP27) in cotranscriptional pre-mRNA processing remains poorly understood. We show that ICP27 promotes cotranscriptional cellular pre-mRNA 3′ end formation using cryptic polyadenylation signals in introns, generating hundreds of novel, intronless GC-rich cellular transcripts that resemble HSV genes. ICP27 also causes aberrant pre-mRNA splicing of some genes. ICP27-targeted genes share common features such as high GC content, cytosine-rich sequences, and suboptimal splice sites, providing an explanation for the observed target specificity of ICP27 and suggesting an overlapping mechanism for ICP27-mediated aberrant pre-mRNA splicing and polyadenylation. By specifically modifying pre-mRNA processing of HSV-like GC-rich transcripts that are likely spared by the virion host shutoff protein, ICP27 contributes to virus-induced host shutoff required for efficient viral growth. The herpes simplex virus (HSV) infected cell culture polypeptide 27 (ICP27) protein is essential for virus infection of cells. Recent studies suggested that ICP27 inhibits splicing in a gene-specific manner via an unknown mechanism. Here, RNA-sequencing revealed that ICP27 not only inhibits splicing of certain introns in <1% of cellular genes, but also can promote use of alternative 5′ splice sites. In addition, ICP27 induced expression of pre-mRNAs prematurely cleaved and polyadenylated from cryptic polyadenylation signals (PAS) located in intron 1 or 2 of ∼1% of cellular genes. These previously undescribed prematurely cleaved and polyadenylated pre-mRNAs, some of which contain novel ORFs, were typically intronless, <2 Kb in length, expressed early during viral infection, and efficiently exported to cytoplasm. Sequence analysis revealed that ICP27-targeted genes are GC-rich (as are HSV genes), contain cytosine-rich sequences near the 5′ splice site, and have suboptimal splice sites in the impacted intron, suggesting that a common mechanism is shared between ICP27-mediated alternative polyadenylation and splicing. Optimization of splice site sequences or mutation of nearby cytosines eliminated ICP27-mediated splicing inhibition, and introduction of C-rich sequences to an ICP27-insensitive splicing reporter conferred this phenotype, supporting the inference that specific gene sequences confer susceptibility to ICP27. Although HSV is the first virus and ICP27 is the first viral protein shown to activate cryptic PASs in introns, we suspect that other viruses and cellular genes also encode this function.
How do general practitioners and patients make decisions about cardiovascular disease risk?

OBJECTIVE Although current guidelines around the world recommend using absolute risk (AR) thresholds to decide whether cardiovascular disease (CVD) risk should be managed with lifestyle or medication, the use of AR in clinical practice is limited. The aim of this study was to explore the factors that influence general practitioner (GP) and patient decision making about CVD risk management, including the role of risk perception. METHODS Qualitative descriptive study involving semi-structured interviews with 25 GPs and 38 patients in Australia in 2011-2012. Transcribed audio-recordings were thematically coded and a Framework Analysis method was used. RESULTS GPs rarely mentioned AR thresholds but were influenced by their subjective perception of the patient's risk and motivation, and their own attitudes toward prevention, including concerns about medication side effects and the efficacy of lifestyle change. Patients were influenced by individual risk factors, their own motivation to change lifestyle, and attitudes toward medication: initially negative, but this improved if medication was more effective than lifestyle. High perceived risk led to medication being recommended by GPs and accepted by patients, but this was not necessarily based on AR. Patient perceptions of high risk also increased motivation to change lifestyle, particularly if they were resistant to the idea of taking medication. CONCLUSIONS Perceived risk, motivation, and attitudes appeared to be more important than AR thresholds in this study. CVD risk management guidelines could be more useful if they include strategies to help GPs consider patients' risk perception, motivation, and attitudes as well as evidence-based recommendations.
Population Genomics in Wild Tomatoes—The Interplay of Divergence and Admixture

Abstract Hybridization between closely related plant species is widespread, but the outcomes of hybridization are not fully understood. This study investigates phylogenetic relationships and the history of hybridization in the wild tomato clade (Solanum sect. Lycopersicon). We sequenced RNA from individuals of 38 different populations and, by combining this with published data, build a comprehensive genomic data set for the entire clade. The data indicate that many taxa are not monophyletic and many individuals are admixed due to repeated hybridization. The most polymorphic species, Solanum peruvianum, has two genetic and geographical subpopulations, while its sister species, Solanum chilense, has distinct coastal populations and reduced heterozygosity indicating a recent expansion south following speciation from S. peruvianum circa 1.25 Ma. Discontinuous populations west of 72° are currently described as S. chilense, but are genetically intermediate between S. chilense and S. peruvianum. Based upon molecular, morphological, and crossing data, we test the hypothesis that these discontinuous “S. chilense” populations are an example of recombinational speciation. Recombinational speciation is rarely reported, and we discuss the difficulties in identifying it and differentiating between alternative demographic scenarios. This discovery presents a new opportunity to understand the genomic outcomes of hybridization in plants.
The Personalized Advantage Index: Translating Research on Prediction into Individualized Treatment Recommendations. A Demonstration

Background Advances in personalized medicine require the identification of variables that predict differential response to treatments as well as the development and refinement of methods to transform predictive information into actionable recommendations. Objective To illustrate and test a new method for integrating predictive information to aid in treatment selection, using data from a randomized treatment comparison. Method Data from a trial of antidepressant medications (N = 104) versus cognitive behavioral therapy (N = 50) for Major Depressive Disorder were used to produce predictions of post-treatment scores on the Hamilton Rating Scale for Depression (HRSD) in each of the two treatments for each of the 154 patients. The patient's own data were not used in the models that yielded these predictions. Five pre-randomization variables that predicted differential response (marital status, employment status, life events, comorbid personality disorder, and prior medication trials) were included in regression models, permitting the calculation of each patient's Personalized Advantage Index (PAI), in HRSD units. Results For 60% of the sample a clinically meaningful advantage (PAI≥3) was predicted for one of the treatments, relative to the other. When these patients were divided into those randomly assigned to their “Optimal” treatment versus those assigned to their “Non-optimal” treatment, outcomes in the former group were superior (d = 0.58, 95% CI .17—1.01). Conclusions This approach to treatment selection, implemented in the context of two equally effective treatments, yielded effects that, if obtained prospectively, would rival those routinely observed in comparisons of active versus control treatments.
Operative Management and Outcomes of 150 Patients with Curative-intent Surgery for Perihilar Cholangiocarcinomas: A Single Institute East European Perspective

Introduction: The knowledge of current approach and outcomes of curative-intent surgery for perihilar cholangiocarcinoma (PHC) has been highlighted in studies of the literature including mainly East Asian and Western patients. Thus, papers presenting the curative-intent surgery in East Europe are scarce. The study aims to present the operative management and outcomes of curative-intent surgery for PHC in an East European institutional experience. Patients and methods: The data of all patients with curative-intent surgery for PHC between 1996 and 2017 were retrospectively reviewed from a prospective maintained electronic database at our Department of Surgery. The assessment was made for the operative management and early and late outcomes. Results: Liver resections were performed in 80.7% of patients, with caudate lobectomies in 64.7% of cases. Vascular resections were performed in 19.4% of patients. Preoperative biliary drainage was performed in 26% of patients. Negative resection margins were obtained in 76.7% of patients. Overall and severe morbidity rates were 57.3% and 24%, respectively. Postoperative bile leak, liver failure and hemorrhage rates were 31.3%, 24.7% and 10%, respectively. The 90-day mortality rate was 6%. The median overall and disease-free survival times were 26 months and 21 months, respectively. Conclusion: The standard approach for curative-intent surgery for PHC implies bile duct resection associated with major hepatectomies, including caudate lobectomy. Expertise in referral surgical centers of East Europe is associated with morbidity, mortality and overall survival rates comparable with those reported in Western centres, despite low rate of preoperative biliary drainage and no use of portal vein embolization. Improvements of preoperative optimization with portal vein embolization and biliary drainage may potentially lead to better early and long-term outcomes.