Miracle-dz/UniFAR-FTUs huggingface dataset:
An integrated systems approach to crop improvement.

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) given the resources available to search among possible combinations in the target population of environments (E). Crop improvement can be viewed as a search strategy on a complex G×M×E adaptation or fitness landscape. Here we consider design of an integrated systems approach to crop improvement that incorporates advanced technologies in molecular markers, statistics, bio-informatics, and crop physiology and modelling. We suggest that such an approach can enhance the efficiency of crop improvement relative to conventional phenotypic selection by changing the focus from the paradigm of identifying superior varieties to a focus on identifying superior combinations of genetic regions and management systems. A comprehensive information system to support decisions on identifying target combinations is the critical core of the approach. We discuss the role of ecophysiology and modelling in this integrated systems approach by reviewing (i) applications in environmental characterization to underpin weighted selection; (ii) complex-trait physiology and genetics to enhance the stability of QTL models by linking the vector of coefficients defining the dynamic model to the genetic regions generating variability; and (iii) phenotypic prediction in the target population of environments to assess the value of putative combinations of traits and management systems and enhance the utility of QTL models in selection. We examine in silico evidence of the value of ecophysiology and modelling to crop improvement for complex traits and note that, while there is no definitive position, it seems clear that there is sufficient promise to warrant continued effort. We discuss criteria determining the nature of models required and argue that a greater degree of biological robustness is required for modelling the physiology and genetics of complex traits. We conclude that, while an integrated systems approach to crop improvement is in its infancy, we expect that the potential benefits and further technology developments will likely enhance its rate of development
Definition of the human immunodeficiency virus type 1 Rev and human T-cell leukemia virus type I Rex protein activation domain by functional exchange

The human retroviruses human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type I (HTLV-I) are characterized by complex regulation of gene expression. Each virus encodes a posttranscriptional regulator, the 19-kDa HIV-1 Rev protein and the 27-kDa HTLV-I Rex protein, which is required for viral replication. Expression of these trans activators results in the cytoplasmic accumulation of unspliced or singly spliced viral mRNA which encode the gag, pol, and env gene products. The finding that the HTLV-I Rex protein is able to functionally substitute for the Rev protein of HIV-1 indicates that HIV-1 Rev and HTLV-I Rex may interact with the same component of a cellular pathway involved in either mRNA splicing or transport. In this study, we have generated functional Rev/Rex hybrid proteins by domain exchange. We have defined, using in vivo and in vitro analyses, the activation domains of Rev and Rex which are the putative targets of a common host cell factor(s) required for Rev and Rex function.
Sylvatic Dengue Viruses Share the Pathogenic Potential of Urban/Endemic Dengue Viruses

Dengue virus (DENV) exists in both sylvatic and urban/endemic ecotypes (15), and the potential for emergence of sylvatic strains has become a focus of research. Recently Mota and Rico-Hesse (10) attempted to evaluate the pathogenic potential of viruses belonging to different genetic subgroups of DENV serotype 2 (DENV-2). Based on the viremia levels and erythema index profiles of one sylvatic genotype and three (Asian, American, and Indian) urban/endemic genotypes evaluated using the NOD-scid IL2rγnull humanized mouse model, the authors concluded that sylvatic DENV-2 viruses possess a reduced pathogenic potential compared to strains belonging to urban/endemic DENV-2 genotypes. However, these conclusions ignore both patterns in their own data and a wealth of published ex vivo, in vivo, and epidemiological evidence collected over the past 40 years.
Odorants specifically modulate chemotaxis and tissue retention of CD4+ T cells via cyclic adenosine monophosphate induction

Retention of T cells within affected tissue is a critical component of adaptive immune inflammation. However, the mechanisms involved in T cell retention remain largely undefined. Previous studies revealed the capacity of cAMP signaling to regulate immune cell migration, as well as dynamic regulation of receptors that could induce cAMP production in immune cells. The potential for cAMP to act as a retention signal has been mostly unexplored, partially as a result of this second messenger's well‐characterized inhibition of effector function in immune cells. Here, we report that cAMP regulates the tissue retention of mouse T cells at concentrations well below those that inhibited proliferation or decreased acquisition of an effector phenotype. Stimulation of CD4+ T cells with odorants known to be cognate ligands for T cell‐expressed olfactory receptors induced cAMP and inhibited chemokine‐driven chemotaxis without decreasing T cell proliferation or effector functions. Similar effects were observed following treatment with relatively low concentrations of the cAMP analog Sp‐5,6‐dichloro‐1‐β‐d‐ribofuranosylbenzimidazole‐3′,5′‐monophosphorothioate. Furthermore, pretreatment with odorants or cAMP at concentrations that did not inhibit effector function induced T cell tissue retention in mice by inhibiting chemokine‐dependent T cell egress from the footpad to the draining lymph node. Together, these results suggest that odorant receptor‐mediated increases in intracellular cAMP can modulate T cell tissue trafficking and may offer new therapeutic targets for controlling T cell tissue accumulation.
A week-by-week analysis of the low-risk criteria for serious bacterial infection in febrile neonates

Objective: To examine the reliability of “low-risk” criteria (LRC) to exclude serious bacterial infection (SBI) in febrile neonates (⩽28 days), according to age in weeks. Design: Epidemiological and clinical data and final diagnosis of all febrile neonates presenting to the emergency room from June 1997 to May 2006 were reviewed. Neonates who fulfilled specific LRC for the presence of SBI were classified as LRC+. The prevalence of SBI and the percentage of LRC+ neonates who had SBI were calculated for each of the first 4 weeks of life. Results: A total of 449 neonates were evaluated. Eighty-seven (19.4%) neonates had an SBI. The prevalence of SBI among infants 3–7, 8–14, 15–21 and 22–28 days of age was 21.6%, 26.1%, 17.9% and 12.1%, respectively (p = 0.007 for linear trend after second week of life). Of the 226 LRC+ neonates, 14 (6.2%) had an SBI, including one case of bacteraemia and meningitis and 13 cases of urinary tract infection (UTI). The negative predictive value (NPV) of the LRC for SBI was 93.8% (95% CI 90.1% to 96.4%). The prevalence of SBI among LRC+ infants 3–7, 8–14, 15–21 and 22–28 days of age was similar, with rates of 15%, 6.3%, 3.0% and 6.7%, respectively. Conclusion: LRC are not sufficiently reliable to exclude the presence of SBI, including bacteraemia and meningitis in febrile neonates of all ages. All febrile neonates should therefore be hospitalised, undergo a full “sepsis evaluation” and receive empirical intravenous antibiotic therapy.
LONG-TERM TRENDS IN INTRAOCULAR PRESSURE AFTER PARS PLANA VITRECTOMY

Purpose: To evaluate the effect of vitrectomy on intraocular pressure (IOP). Methods: Retrospective cohort study. Medical records of 101 eyes of 101 patients undergoing nonemergent vitrectomy were reviewed for rates of open-angle glaucoma, increased IOP of >4 mmHg from baseline, change in IOP from baseline, and cataract formation. Preoperative and last measured IOPs were recorded. Baseline risk characteristics including lens status and diabetes were analyzed. Main outcome measures were 1) incidence of open-angle glaucoma; 2) increase in IOP of >4 mmHg; and 3) change in IOP. Results: Mean follow-up was 49 months (range, 12-105 months). Mean baseline IOP was 15.3 mmHg, and mean final IOP was 15.8 mmHg (P = 0.3). At the most recent examination, 35 study eyes had a decrease in IOP from baseline, while 14 eyes had no change and 52 eyes had an increase in IOP. Four study eyes were newly diagnosed with ocular hypertension. No study eye developed open-angle glaucoma or required medical, laser, or surgical treatment for glaucoma. Incidence of increased IOP of >4 was 7% at 4 years and 34% at 8 years. Subgroup analysis of 66 patients comparing study eyes with nonvitrectomized fellow eyes demonstrated no significant difference in rates of increased IOP of >4 (P = 0.85). Neither diabetes nor pseudophakia was associated with significantly increased IOP. Conclusion: In this series, vitrectomy does not appear to increase IOP even after removal of the crystalline lens.
Threshold attribute-based encryption with attribute hierarchy for lattices in the standard model

Attribute-based encryption (ABE) has been considered as a promising cryptographic primitive for realising information security and flexible access control. However, the characteristic of attributes is treated as the identical level in most proposed schemes. Lattice-based cryptography has been attracted much attention because of that it can resist to quantum cryptanalysis. In this study, lattice-based threshold hierarchical ABE (lattice-based t -HABE) scheme without random oracles is constructed and proved to be secure against selective attribute set and chosen plaintext attacks under the standard hardness assumption of the learning with errors problem. The notion of the HABE scheme can be considered as the generalisation of traditional ABE scheme where all attributes have the same level.
Continuous Infusion of Ketamine for Out-of-hospital Isolated Orthopedic Injuries Secondary to Trauma: A Randomized Controlled Trial

Abstract Objective. Although ketamine has recently been demonstrated to provide a morphine-sparing effect, no previous study reports the effect of continuous infusion of ketamine for analgesia in out-of-hospital environments. The aim of this study was to compare the effect of a continuous infusion of ketamine (IK group) vs. a continuous infusion of saline (IS group) on morphine requirements in out-of-hospital trauma patients suffering from severe acute pain. Methods. In this prospective, multicenter, randomized, single-blind clinical study, patients suffering from isolated orthopedic injuries secondary to trauma with severe acute pain received a low-dose intravenous (IV) bolus of ketamine (0.2 mg·kg−1) combined with an IV bolus of morphine (0.1 mg·kg−1) and were randomized either in the IK group (IV continuous infusion of ketamine 0.2 mg·kg−1·h−1), or in the IS group (IV continuous infusion of saline at the same volume). The primary endpoint was morphine requirements in terms of total dose of morphine (excluding the baseline bolus) injected at the end of prehospital emergency care at hospital admission (final time, Tf). The secondary endpoint was evaluation of pain with visual analogic scale (VAS). Results. Sixty-six patients were enrolled. Total morphine dose was not significantly reduced with continuous infusion of ketamine (0.048 [0.000; 0.150] vs. 0.107 [0.052; 0.150] in IK and IS groups), with similar mean duration of care (median 35.0 min). Analgesia was as efficient without any significant difference in VAS at Tf between groups (3.1 ± 2.3 (IK group) vs. 3.7 ± 2.7 (IS group), p = 0.5). Conclusions. Continuous ketamine infusion did not reduce morphine requirements in severe acute pain trauma patients in the out-of-hospital emergency settings.
Routes to formation of highly excited neutral atoms in the breakup of strongly driven H 2

We present a theoretical quasiclassical treatment of the formation, during Coulomb explosion, of highly excited neutral H atoms (${\text{H}}^{*}$) for strongly driven ${\text{H}}_{2}$. This process, where after the laser field is turned off, one electron escapes to the continuum while the other occupies a Rydberg state, was recently reported in an experimental study [B. Manschwetus et al., Phys. Rev. Lett. 102, 113002 (2009)]. We find that two-electron effects are important in order to correctly account for all pathways leading to ${\text{H}}^{*}$ formation. We identify two pathways where the electron that escapes to the continuum does so either very quickly or after remaining bound for a few periods of the laser field. These two pathways of H${}^{*}$ formation have distinct traces in the probability distribution of the escaping electron momentum components.
Overview of the Second BUCC Shared Task: Spotting Parallel Sentences in Comparable Corpora

This paper presents the BUCC 2017 shared task on parallel sentence extraction from comparable corpora. It recalls the design of the datasets, presents their final construction and statistics and the methods used to evaluate system results. 13 runs were submitted to the shared task by 4 teams, covering three of the four proposed language pairs: French-English (7 runs), German-English (3 runs), and Chinese-English (3 runs). The best F-scores as measured against the gold standard were 0.84 (German-English), 0.80 (French-English), and 0.43 (Chinese-English). Because of the design of the dataset, in which not all gold parallel sentence pairs are known, these are only minimum values. We examined manually a small sample of the false negative sentence pairs for the most precise French-English runs and estimated the number of parallel sentence pairs not yet in the provided gold standard. Adding them to the gold standard leads to revised estimates for the French-English F-scores of at most +1.5pt. This suggests that the BUCC 2017 datasets provide a reasonable approximate evaluation of the parallel sentence spotting task.
Treatment of Port-Wine Stains with the Flashlamp-pumped Pulsed Dye Laser: Extended Clinical Experience in Children and Adults

Seventy-six patients (51 females, 25 males) with port-wine stains (PWS) were treated with the flashlamp-pumped pulsed dye laser (585 nm, 450 μsec). The patients ranged in age from 1 month to 71 years (average, 14 yr). Forty-nine percent of all patients under study had a 90% or better (average, 94.6%) lightening response after an average of 9.0 (range, 4-15) laser treatments. Overall, there was a 79% clinical improvement seen after an average of 9.1 (range, 2-19) laser treatments. In contrast to previous studies, the number of treatments necessary to obtain PWS clearing in older children (9–15 yr) and adults (>16 yr) was not significantly greater than the number required to treat PWS in infants ( 0–2 yr) and younger children ( 3–8 yr). In fact, PWS in children aged 3 to 8 years required the greatest number of laser treatments, which may be due to continued abnormal growth of the ectatic blood vessels comprising the lesion during the growth of the child. In addition, there did not appear to be a significant difference in the number of laser treatments necessary to obtain clearing of PWS in different body locations. While the 585 nm pulsed dye laser continues to be the treatment of choice for removal of PWS in children and adults, the number of treatments necessary to obtain lesional clearing in all age groups is greater than previously reported.
Poorly differentiated adenocarcinoma and mucinous carcinoma of the colon and rectum show higher rates of loss of heterozygosity and loss of E‐cadherin expression due to methylation of promoter region

Previous studies have reported that poorly differentiated adenocarcinoma and mucinous carcinoma of the colon and rectum (Por & Muc) show a low incidence and poor prognosis. However, genetic alterations and tumourigenesis of Por & Muc remain unclear. In our study, we analyzed the genetic and epigenetic alterations of Por & Muc to clarify the difference from those of well‐differentiated adenocarcinoma (WD). First, we evaluated the loss of heterozygosity (LOH) on 4 chromosomes (2p, 5q, 17p, 18q) frequently observed in colorectal cancer. Second, to determine large‐scale allelic losses, we performed wide‐ranging allelotyping study. Using 27 microsatellite markers spanning every 10 cM on chromosome 17 and 18, we defined the LOH ratio as the proportion of markers that exhibit LOH out of 27 markers. Third, we evaluated the methylation of E‐cadherin. With respect to LOH of 4 loci, higher rates of LOH were observed in Por & Muc and a statistical significance was found on the markers adjacent to MSH2 and SMAD4/DCC. Moreover, as the evidence of large‐scale allelic imbalance, the average LOH ratio was higher in Por & Muc (0.70) than in WD (0.24) (p = 0.01). Methylation analysis showed that 54.5% of Por & Muc demonstrated hypermethylation of E‐cadherin. In immunohistochemistry, 77.8% of Por & Muc exhibited abnormal expression of E‐cadherin. Hypermethylation of E‐cadherin correlated significantly with abnormal expression (p = 0.047). These results suggest that the higher rates of LOH contribute to Por & Muc tumourigenesis and most of Por & Muc lose normal E‐cadherin expression, partly because of the methylation of promoter region. © 2002 Wiley‐Liss, Inc.
Improving the reproducibility of voluntary deep inspiration breath hold technique during adjuvant left-sided breast cancer radiotherapy

Abstract Background: Adjuvant radiotherapy (RT) of left-sided breast cancer (LSBC) with voluntary deep inspiration breath hold (vDIBH) technique reduces the cardiac dose. In this study, the effect of marker block position and the efficacy of breath hold level (BHL) correction based on lateral kV setup images are evaluated to improve the daily reproducibility. Material and methods: A total of 148 consecutive LSBC patients treated with vDIBH RT were included in this study. The real-time position management (RPM) marker block was placed on the abdominal wall in 63 patients (group A) and on the sternum in 85 patients (group S). Acquired 900 (group A) + 1040 (group S) orthogonal image pairs were retrospectively analyzed. The actual BHL was determined from the lateral kV images. The height of the BHL gating window in RPM was corrected if errors of the actual BHL exceeded 4 mm. Setup margins were calculated for the chest wall and for bony surrogates of the lymph node regions. Results: The sternal marker block reduced the random residual errors in the actual BHL (p < 0.05). The BHL correction was required for 26/63 patients in group A and for 26/85 patients in group S. Correction of the BHL window significantly reduced both the systematic and the random residual error in both groups. In patients with lymph node irradiation, the effect of both marker placement and BHL window correction was significant in the superior-inferior direction. Correction of the BHL reduced the mean cardiac dose by 0.5 Gy (p < 0.01) in group A and 0.6 Gy (p < 0.05) in group S. Conclusions: Reproducibility of the BHL can be improved by placing the marker block on the sternum and correcting the height of the BHL window based on lateral kV setup images. Acquisition of lateral kV images in the first 3 fractions and once a week during RT is recommended.
Nucleotide sequence and cloning in Bacillus subtilis of the Bacillus stearothermophilus pleiotropic regulatory gene degT

The regulatory gene (degT) from Bacillus stearothermophilus NCA1503 which enhanced production of extracellular alkaline protease (Apr) was cloned in Bacillus subtilis with pTB53 as a vector. When B. subtilis MT-2 (Npr- [deficiency of neutral protease] Apr+) was transformed with the recombinant plasmid, pDT145, the plasmid carrier produced about three times more alkaline protease than did the wild-type strain. In contrast, when B. subtilis DB104 (Npr- Apr-) was used as a host, the transformant with pDT145 could not exhibit any protease activity. After construction of the deletion plasmids, DNA sequencing was done. A large open reading frame was found, and nucleotide sequence analysis showed that the degT gene was composed of 1,116 bases (372 amino acid residues, molecular weight of 41,244). A Shine-Dalgarno sequence was found nine bases upstream from the open reading frame. A B. subtilis strain carrying degT showed the following pleiotropic phenomena: (i) enhancement of production of extracellular enzymes such as alkaline protease and levansucrase, (ii) repression of autolysin activity, (iii) decrease of transformation efficiency for B. subtilis (competent cell procedure), (iv) altered control of sporulation, (v) loss of flagella, and (vi) abnormal cell division. When B. stearothermophilus SIC1 was transformed with the recombinant plasmid carrying degT, the transformants exhibited abnormal cell division. These phenomena are similar to those of the phenotypes of degSU(Hy) (hyperproduction), degQ(Hy), and degR mutants of B. subtilis. However, the amino acid sequence of the degT product (DegT) is different from those of the reported gene products. Furthermore, DegT includes a hydrophobic core region in the N-terminal portion (amino acid numbers 50 to 160), a consensus sequence for a DNA binding region (amino acid numbers 160 to 179), and a region homologous to transcription activator proteins (amino acid numbers 351 to 366). We discuss the possibility that the membrane protein DegT functions as a sensor protein and transfers the signal of environmental stimuli to the regulatory region of target genes to activate or repress transcription of the genes.
Expanding the SHOC2 mutation associated phenotype of noonan syndrome with loose anagen hair: Structural brain anomalies and myelofibrosis

Noonan syndrome is a heterogenous rasopathy typically presenting with short stature, characteristic facial features, cardiac abnormalities including pulmonic valve stenosis, ASD and hypertrophic cardiomyopathy (HCM), cryptorchidism, ectodermal abnormalities, and learning differences. The phenotype is variable, and limited genotype phenotype correlation exists with SOS1 mutations often associated with normal cognition and stature, RAF1 mutations entailing a high HCM risk, and certain PTPN11 mutations predisposing to juvenile myelomonocytic leukemia. The recently identified SHOC2 mutation (p.Ser2Gly) causes Noonan syndrome with loose anagen hair. We report five patients with this mutation. All had skin hyperpigmentation, sparse light colored hair, increased fine wrinkles, ligamentous laxity, developmental delay, and 4/4 had a structural cardiac anomaly. Hypotonia and macrocephaly occurred in 4/5 (80%); 3/5 (60%) had polyhydramnios, increased birth weight or required use of a feeding tube. Distinctive brain abnormalities included relative megalencephaly and enlarged subarachnoid spaces suggestive of benign external hydrocephalus, and a relatively small posterior fossa as indicated by a vertical tentorium. The combination of a large brain with a small posterior fossa likely resulted in the high rate of cerebellar tonsillar ectopia (3/4; 75%). Periventricular nodular heterotopia was seen in one patient with a thick and dysplastic corpus callosum. We report on the first hematologic neoplasm, myelofibrosis, in a 2‐year‐old patient with SHOC2 mutation. Myelofibrosis is exceedingly rare in children and young adults. The absence of a somatic JAK2 mutation, seen in the majority of patients with myelofibrosis, is noteworthy as it suggests that germline or somatic SHOC2 mutations are causally involved in myelofibrosis. © 2013 Wiley Periodicals, Inc.