Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phylogenetic comparative (PC) analyses, we define the timeline of TAP loss, gain, and expansion among Viridiplantae and find that two major bursts of gain/expansion occurred, coinciding with the water-to-land transition and the radiation of flowering plants. For the first time, we provide PC proof for the long-standing hypothesis that TAPs are major driving forces behind the evolution of morphological complexity, the latter in Plantae being shaped significantly by polyploidization and subsequent biased paleolog retention. Principal component analysis incorporating the number of TAPs per genome provides an alternate and significant proxy for complexity, ideally suited for PC genomics. Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity.
Safety and Immunogenicity of a New Trivalent Inactivated Split-virus Influenza Vaccine in Healthy Korean Children: A Randomized, Double-blinded, Active-controlled, Phase III Study

We report results of a randomized, double-blinded, active-controlled, phase III study conducted to evaluate the immunogenicity and safety of a new trivalent inactivated split-virus influenza vaccine (GC501) manufactured by the Green Cross Corporation in Korea. A total of 283 healthy children aged 6 months to < 18 yr were randomized to receive either GC501 or control. Of the GC501 recipients, seroconversion occurred in 48.5% for A/H1N1, 67.7% for A/H3N2 and 52% for influenza B. The proportion of subjects who had post-vaccination hemagglutination-inhibition titers of 1:40 or greater was 90.7% for A/H1N1, 86.8% for A/H3N2 and 82.4% for influenza B in the GC501 recipients. No serious adverse events related to vaccination, or withdrawals because of adverse events were reported. The majority of solicited adverse events were mild in intensity. GC501 vaccine has good tolerability and favorable immunogenicity in children aged 6 months to < 18 yr. The addition of one more brand of influenza vaccine may allow for better global accessibility of vaccine for epidemics or future pandemics.
Optimal Portfolio and Equity Premium Puzzle

Portfolio with one risk-free and one risky assets was explored in \cite{BT1995, LO1999, SS2000, Gomes2005, Bassett2004, DGP2008, BG2009, HZ2009} for risk averse investors. Most of them, for example, \cite{BT1995, LO1999, SS2000, Gomes2005, Bassett2004, DGP2008} focus on empirical or numerical studies, except for some optimization problems solved simply by heuristics. Some analytical treatments have been carried out for single period portfolio choice models, and closed-form solutions were obtained for a number of interesting cases, see, for example, \cite{BG2009,HZ2009}. Since investors' risk aversion is of first order \cite{EZ1990}, known results in \cite{Gomes2005} are constraint. Considering investors' general risk aversion, this paper models portfolio with one risk-free and one risky assets for risk averse investors with general value functions, including specific power utility or risk of first order, explores optimal portfolio choice analytically, then interprets equity premium puzzle. Since this paper treats with general value functions including, in particular, ones of constant relative risk aversion, our results generalizes \cite{BT1995, LO1999, SS2000, Gomes2005, Bassett2004, BKP2004, DGP2008} on single period portfolio choice.
Tensor Deflation for CANDECOMP/PARAFAC— Part I: Alternating Subspace Update Algorithm

CANDECOMP/PARAFAC (CP) approximates multiway data by sum of rank-1 tensors. Unlike matrix decomposition, the procedure which estimates the best rank- R tensor approximation through R sequential best rank-1 approximations does not work for tensors, because the deflation does not always reduce the tensor rank. In this paper, we propose a novel deflation method for the problem. When one factor matrix of a rank- R CP decomposition is of full column rank, the decomposition can be performed through (R-1) rank-1 reductions. At each deflation stage, the residue tensor is constrained to have a reduced multilinear rank. For decomposition of order-3 tensors of size R×R×R and rank- R, estimation of one rank-1 tensor has a computational cost of O(R3) per iteration which is lower than the cost O(R4) of the ALS algorithm for the overall CP decomposition. The method can be extended to tracking one or a few rank-one tensors of slow changes, or inspect variations of common patterns in individual datasets.
A Chemistry-Inspired Middleware for Self-Adaptive Service Orchestration and Choreography

Orchestration and choreography are two perspectives to model service interactions in executing a service composition. Compared to orchestration model, choreography can improve the performances in scalability, throughput and execution time by eliminating centralized point of coordination. However, it also brings additional complexities and challenges such as inter-organizational service coordination, fault-tolerance and etc. In this paper, we propose two self-managed and self-adaptive choreography models, namely semi-choreography and auto-choreography. Both models as well as a centralized orchestration model have been implemented in a chemistry-inspired middleware. With the metaphor from chemical reactions, the middleware is modeled as an autonomic distributed chemical system, where services are described as complex molecules and service coordination and adaptation is performed by a series of pervasive chemical reactions controlled by a number of rules. By using different sets of rules, providers are able to specify their preferred execution models to run service compositions, in either centralized or collaborative way. The middleware is implemented in Higher-Order Chemical Language (HOCL) and running on distributed infrastructures (Grid'5000). Finally, by executing two experimental workflows in the middleware, a number of experiments have been conducted to evaluate and compare different models in terms of complexity and efficiency.
Mirror, mirror in my hand: a duality between specifications and models of process behaviour

Summary Since Pnueli’s seminal paper in 1977, Temporal Logic has been used as a formalism for specifying and verifying the correctness of reactive systems. In this paper, we show that, besides its expressive power, Temporal Logic enjoys a very strong structural property: it is categorical on processes. That is, we show how temporal specifications (as theories) can be embedded in categories of process behaviour, and out of this adjunction we build an institution that is categorical in the sense of Meseguer. This characterisation means that temporal logic is, in a sense, ‘sound and complete’ with respect to process specification and interconnection techniques.
Time-dependency of human lactate dehydrogenase isoenzyme 5 inhibition by urea.

Urea, in low concentrations, is known to be an in vitro competitive inhibitor of human lactate dehydrogenase [EC 1.1. 1.27; LD] activity; as the concentration of urea is increased the effect is that of a denaturing agent (1, 2). The inhibition effect is greatest on LD-5, and urea has therefore been used to estimate the amount of anodic LD isoenzymes present.in a serum specimen (3-6) as a diagnostic test for myocardial infarction. While establishing our own conditions for this test we encountered a timedependency effect of the inhibition of human LD-5, that to our knowledge has not previously been described. All enzyme assays were done with the LKB 8600 Reaction Rate Analyzer at 37.0 #{176}C (LKB Instruments, Inc., Rockville, Md. 20852). Specimens were assayed by the LD method described by the Committee on Enzymes of the Scandinavian Society for Clinical Chemistry and Clinical Physiology (7) except that when urea was present in the assay the final pyruvate concentration was 3 mmol/liter. The diluted specimen was immediately placed in the incubation tunnel of the Reaction Rate Analyzer. When the effect of time of exposure to urea was being investigated for short time intervals, the assay solution and specimen were separately pre-incubated, at 37 #{176}C, and then the specimen was rapidly diluted into the reaction cuvette. The cuvette was then inserted directly into the cuvette holder maintained at a temperature of 37 #{176}C within the incubation tunnel. The time from specimen dilution to initiation of the reaction rate assay was timed by stopwatch. By this technique the first reading was made 3 mm after specimen dilution. Human heart and liver, stored at -80 #{176}C until required, were used as sources of semipurified LD-1 and LD-5, respectively. The preparation of these isoenzymes has been described (8). The isoenzymes were suspended in the preparation buffer containing 30 g of bovine serum albumin per liter (final concentration). Figure 1 shows the effect of urea concentration on semipurified LD-1 and LD-5. These results are very similar to those obtained by other workers (4-6,9, 10), although many used liver and heart homogenates. When the effect of time of pre-incubation of LD-5 in the urea/buffer medium is taken into account, it is clear that 1 mol of urea per liter can inhibit LD-5 by 90% (Figure 2). The approximate t112 for this reaction is 5 min, which probably explains why this effect does not seem to have been detected by others. The effect is not due to heat inactivation (Figure 2). Two groups (5, 10) used 30 #{176}C and pyruvate substrate but neither reported
Clinical Characteristics of the Suicide Attempters Who Refused to Participate in a Suicide Prevention Case Management Program

Case management interventions for suicide attempters aimed at helping adjust their social life to prevent reattempts have high nonparticipation and dropout rates. We analyzed the clinical characteristics of the group who refused to participate in the suicide prevention program in Korea. A total of 489 patients with a suicide attempt who visited Uijeongbu St. Mary's Hospital, the Catholic University of Korea, from December 2009 to December 2013 were analyzed. All patients were divided into the participation group (n = 262) and the refusal group (n = 227) according to their participation in the case management program. Demographic and clinical characteristics of each group were examined. Results showed that the refusal group had low risks for suicide in terms of risk factors related with psychopathologies and presenting suicide behavior. That is, the refusal group had less patients with co-morbid medical illnesses and more patients with mild severity of depression compared to the participation group. However, the refusal group had more interpersonal conflict, more isolation of social integrity, and more impaired insight about suicide attempt. The results suggest that nonparticipation in the case management program may depend upon the patient's impaired insight about the riskiness of suicide and lack of social support. Graphical Abstract
Vector field processing on triangle meshes

While scalar fields on surfaces have been staples of geometry processing, the use of tangent vector fields has steadily grown in geometry processing over the last two decades: they are crucial to encoding directions and sizing on surfaces as commonly required in tasks such as texture synthesis, non-photorealistic rendering, digital grooming, and meshing. There are, however, a variety of discrete representations of tangent vector fields on triangle meshes, and each approach offers different tradeoffs among simplicity, efficiency, and accuracy depending on the targeted application. This course reviews the three main families of discretizations used to design computational tools for vector field processing on triangle meshes: face-based, edge-based, and vertex-based representations. In the process of reviewing the computational tools offered by these representations, we go over a large body of recent developments in vector field processing in the area of discrete differential geometry. We also discuss the theoretical and practical limitations of each type of discretization, and cover increasingly-common extensions such as n-direction and n-vector fields. While the course will focus on explaining the key approaches to practical encoding (including data structures) and manipulation (including discrete operators) of finite-dimensional vector fields, important differential geometric notions will also be covered: as often in Discrete Differential Geometry, the discrete picture will be used to illustrate deep continuous concepts such as covariant derivatives, metric connections, or Bochner Laplacians.
Maternal Macronutrient Intake and Offspring Blood Pressure 20 Years Later

Background Results from 2 cohort studies in Scotland established in the 1940s and 1950s (Aberdeen and Motherwell) suggested that a high protein diet during pregnancy might adversely influence offspring blood pressure at adult age. Our objective was to examine this association in the Danish Fetal Origins Cohort (DaFO88). Methods and Results This was a prospective birth cohort of 965 women who gave birth in 1988–1989 in Aarhus, Denmark, and whose offspring (n=434) participated in a clinical examination ≈20 years later. Macronutrient intake was assessed in gestational week 30. Multivariable adjusted linear regression was used to examine the relation between higher maternal protein intake, at the expense of carbohydrates, and offspring blood pressure (isocaloric substitution). Main analyses were adjusted for mother's age during pregnancy, prepregnancy body mass index, parity, smoking during pregnancy, educational level, and offspring's sex. The mean total energy intake was 8.7 MJ/day (SD 2.3 MJ/day). The mean energy from carbohydrate, fat, and protein intake was 51, 31, and 16 of total energy, respectively. The results showed that after adjustment, higher maternal protein intake was associated with slightly higher offspring diastolic blood pressure (highest compared with the lowest quintile of protein intake: ∆=2.4 mm Hg; 95% CI 0.4–4.4; P=0.03 for trend). Similar differences, although not significant, were found for systolic blood pressure (∆=2.6 mm Hg; 95% CI −0.0 to 5.3; P=0.08 for trend). Conclusions Higher maternal dietary protein intake at the expense of carbohydrates was associated with a modest increase in offspring blood pressure in young adulthood.
Evaluation of Two Line Probe Assays for Rapid Detection of Mycobacterium tuberculosis, Tuberculosis (TB) Drug Resistance, and Non-TB Mycobacteria in HIV-Infected Individuals with Suspected TB

ABSTRACT Limited performance data from line probe assays (LPAs), nucleic acid tests used for the rapid diagnosis of tuberculosis (TB), nontuberculosis mycobacteria (NTM), and Mycobacterium tuberculosis drug resistance are available for HIV-infected individuals, in whom paucibacillary TB is common. In this study, the strategy of testing sputum with GenoType MTBDRplus (MTBDR-Plus) and GenoType Direct LPA (Direct LPA) was compared to a gold standard of one mycobacterial growth indicator tube (MGIT) liquid culture. HIV-positive (HIV+) individuals with suspected TB from southern Africa and South America with <7 days of TB treatment had 1 sputum specimen tested with Direct LPA, MTBDR-Plus LPA, smear microscopy, MGIT, biochemical identification of mycobacterial species, and culture-based drug-susceptibility testing (DST). Of 639 participants, 59.3% were MGIT M. tuberculosis culture positive, of which 276 (72.8%) were acid-fast bacillus (AFB) smear positive. MTBDR-Plus had a sensitivity of 81.0% and a specificity of 100%, with sensitivities of 44.1% in AFB smear-negative versus 94.6% in AFB smear-positive specimens. For specimens that were positive for M. tuberculosis by MTBDR-Plus, the sensitivity and specificity for rifampin resistance were 91.7% and 96.6%, respectively, and for isoniazid (INH) they were 70.6% and 99.1%. The Direct LPA had a sensitivity of 88.4% and a specificity of 94.6% for M. tuberculosis detection, with a sensitivity of 72.5% in smear-negative specimens. Ten of 639 MGIT cultures grew Mycobacterium avium complex or Mycobacterium kansasii, half of which were detected by Direct LPA. Both LPA assays performed well in specimens from HIV-infected individuals, including in AFB smear-negative specimens, with 72.5% sensitivity for M. tuberculosis identification with the Direct LPA and 44.1% sensitivity with MTBDR-Plus. LPAs have a continued role for use in settings where rapid identification of INH resistance and clinically relevant NTM are priorities.
Genetic documentation of filial cannibalism in nature

Cannibalism is widespread in natural populations of fishes, where the stomachs of adults frequently contain conspecific juveniles. Furthermore, field observations suggest that guardian males routinely eat offspring from their own nests. However, recent genetic paternity analyses have shown that fish nests often contain embryos not sired by the nest-tending male (because of cuckoldry events, egg thievery, or nest piracy). Such findings, coupled with the fact that several fish species have known capabilities for distinguishing kin from nonkin, raise the possibility that cannibalism by guardian males is directed primarily or exclusively toward unrelated embryos in their nests. Here, we test this hypothesis by collecting freshly cannibalized embryos from the stomachs of several nest-tending darter and sunfish males in nature and determining their genetic parentage by using polymorphic microsatellite markers. Our molecular results clearly indicate that guardian males do indeed consume their own genetic offspring, even when unrelated (foster) embryos are present within the nest. These data provide genetic documentation of filial cannibalism in nature. Furthermore, they suggest that the phenomenon may result, at least in part, from an inability of guardians to differentiate between kin and nonkin within their own nests.
Long‐term changes in vocal quality following isshiki thyroplasty type I

Long‐term changes in vocal quality, pre‐Isshiki thyroplasty type I and up to 4 years 4 months post‐thyroplasty, were determined in a group of five subjects exhibiting unilateral vocal fold paralysis. Thyroplasty type I medializes the paralyzed fold by using a Silastic® implant for external compression of the paralyzed vocal fold. No periphonosurgical or post‐phonosurgical complications were noted. Longitudinal evaluation resulted in significantly higher vocal fundamental frequency, significant moderation of habitual vocal intensity, and significantly longer maximum phonation time. The thyroplasty group exhibited significantly more breath groups than control subjects both prethyroplasty and post‐thyroplasty; within the thyroplasty group, a reduction in breath groups was exhibited prethyroplasty as compared to post‐thyroplasty. The long‐term positive changes observed in fundamental frequency, intensity, maximum phonation time, and breath groups were attributed to medialization of the paralyzed vocal fold.
Characterization of Novel Cutaneous Human Papillomavirus Genotypes HPV-150 and HPV-151

DNA from two novel HPV genotypes, HPV-150 and HPV-151, isolated from hair follicles of immuno-competent individuals, was fully cloned, sequenced and characterized. The complete genomes of HPV-150 and HPV-151 are 7,436-bp and 7,386-bp in length, respectively. Both contain genes for at least six proteins, namely E6, E7, E1, E2, L2, L1, as well as a non-coding upstream regulatory region located between the L1 and E6 genes: spanning 416-bp in HPV-150 (genomic positions 7,371 to 350) and 322-bp in HPV-151 (genomic positions 7,213 to 148). HPV-150 and HPV-151 are phylogenetically placed within the Betapapillomavirus genus and are most closely related to HPV-96 and HPV-22, respectively. As in other members of this genus, the intergenic E2-L2 region is very short and does not encode for an E5 gene. Both genotypes contain typical zinc binding domains in their E6 and E7 proteins, but HPV-151 lacks the regular pRb-binding core sequence within its E7 protein. In order to assess the tissue predilection and clinical significance of the novel genotypes, quantitative type-specific real-time PCR assays were developed. The 95% detection limits of the HPV-150 and HPV-151 assays were 7.3 copies/reaction (range 5.6 to 11.4) and 3.4 copies/reaction (range 2.5 to 6.0), respectively. Testing of a representative collection of HPV-associated mucosal and cutaneous benign and malignant neoplasms and hair follicles (total of 540 samples) revealed that HPV-150 and HPV-151 are relatively rare genotypes with a cutaneous tropism. Both genotypes were found in sporadic cases of common warts and SCC and BCC of the skin as single or multiple infections usually with low viral loads. HPV-150 can establish persistent infection of hair follicles in immuno-competent individuals. A partial L1 sequence of a putative novel HPV genotype, related to HPV-150, was identified in a squamous cell carcinoma of the skin obtained from a 64-year old immuno-compromised male patient.
Extensive Left Temporal Pole Damage Does Not Impact on Theory of Mind Abilities

The temporal poles (TPs) are among the brain regions that are often considered as the brain network sustaining our ability to understand other people's mental states or “Theory of Mind” (ToM). However, so far the functional role of the left and right TPs in ToM is still debated, and it is even not clear yet whether these regions are necessary for ToM. In this study, we tested whether the left TP is necessary for ToM by assessing the mentalizing abilities of a patient (C.M.) diagnosed with semantic dementia. Converging evidence from detailed MRI and 18F-fluoro-2-deoxy-d-glucose PET examinations showed a massive atrophy of the left TP with the right TP being relatively unaffected. Furthermore, C.M. 's atrophy encompassed most regions of the left TP usually activated in neuroimaging studies investigating ToM. Given C.M. 's language impairments, we used a battery of entirely nonverbal ToM tasks. Across five tasks encompassing 100 trials, which probed the patient's ability to attribute various mental states (intentions, knowledge, and beliefs), C.M. showed a totally spared performance. This finding suggests that, despite its consistently observed activation in neuroimaging studies involving ToM tasks, the left TP is not necessary for ToM reasoning, at least in nonverbal conditions and as long as its right counterpart is preserved. Implications for understanding the social abilities of patients with semantic dementia are discussed.