Miracle-dz/UniFAR-FTUs huggingface dataset:
An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications

Transposons are mobile genetic elements and have been utilized as essential tools in genetics over the years. Though highly useful, many of the current transposon-based applications suffer from various limitations, the most notable of which are: (i) transposition is performed in vivo, typically species specifically, and as a multistep process; (ii) accuracy and/or efficiency of the in vivo or in vitro transposition reaction is not optimal; (iii) a limited set of target sites is used. We describe here a genetic analysis methodology that is based on bacteriophage Mu DNA transposition and circumvents such limitations. The Mu transposon tool is composed of only a few components and utilizes a highly efficient and accurate in vitro DNA transposition reaction with a low stringency of target preference. The utility of the Mu system in functional genetic analysis is demonstrated using restriction analysis and genetic footprinting strategies. The Mu methodology is readily applicable in a variety of current and emerging transposon-based techniques and is expected to generate novel approaches to functional analysis of genes, genomes and proteins.
Open Access Review

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Review Reproductive outcome after hysteroscopic septoplasty in patients with septate uterus-a retrospective cohort study and systematic review of the literature Abstract Background: Septate uterus, one of the most common forms of congenital uterine malformations, negatively affects female reproductive health. Methods: In a retrospective cohort study, we evaluated the reproductive outcome after hysteroscopic septoplasty in 64 women with septate uterus and primary or secondary infertility. We performed a systematic review of studies evaluating the reproductive outcome after hysteroscopic septoplasty. Results: Sixty-four women underwent hysteroscopic septoplasty. In 2/64 (3%) women, intraoperative uterine perforation occurred. Complete follow-up was available for 49/64 (76%) patients. Mean follow-up time was 68.6 +/-5.2 months. The overall pregnancy rate after hysteroscopic septoplasty was 69% (34/49). The overall life birth rate (LBR) was 49% (24/49). The mean time interval between surgery and the first life birth was 35.8 +/-22.5 months. Including our own data, we identified 18 studies investigating the effect of septoplasty on reproductive outcome in 1501 women. A pooled analysis demonstrated that hysteroscopic septoplasty resulted in an overall pregnancy rate of 60% (892/1501) and a LBR of 45% (686/1501). The overall rate of intra-and postoperative complications was 1.7% (23/1324) and the overall rate of re-hysteroscopy was 6% (79/1324). Conclusions: In women with septate uterus and a history of infertility, hysteroscopic septoplasty is a safe and effective procedure resulting in a pregnancy rate of 60% and a LBR of 45%. Background Septate uterus, i.e. an incompletely septated uterus or uterus subseptus, is one of the most common forms of congenital uterine malformations [1]. The incidence of congenital uterine malformations has been reported to be as high as 3-4% in the general female population [2,3] and to be significantly higher in patients with infertility and recurrent pregnancy loss [3,4]. Septate uterus results from incomplete resorption of the paramesonephric muellerian ducts during the first trimester of pregnancy. The absorption of the septum normally initiates at the level of the uterine cervix and continues upwards in the direction of the uterine fundus.
Serum Proteome and Cytokine Analysis in a Longitudinal Cohort of Adults with Primary Dengue Infection Reveals Predictive Markers of DHF

Background Infections caused by dengue virus are a major cause of morbidity and mortality in tropical and subtropical regions of the world. Factors that control transition from mild forms of disease such as dengue fever (DF) to more life-threatening forms such as dengue hemorrhagic fever (DHF) are poorly understood. Consequently, there are no reliable methods currently available for early triage of DHF patients resulting in significant over-hospitalization. Methodology/Principal Findings We have systematically examined the proteome, cytokines and inflammatory markers in sera from 62 adult dengue patients (44 DF; 18 DHF) with primary DENV infection, at three different times of infection representing the early febrile, defervescence and convalescent stages. Using fluorescent bioplex assays, we measured 27 cytokines in these serum samples. Additionally, we used multiple mass spectrometry methods for iTRAQ-based comparative analysis of serum proteome as well as measurements of protein adducts- 3-nitrotyrosine and 3-chlorotyrosine as surrogate measures of free radical activity. Using multiple methods such as OPLS, MRMR and MSVM-RFE for multivariate feature selection and classification, we report molecular markers that allow prediction of primary DHF with sensitivity and specificity of >80%. Conclusions/Significance This report constitutes a comprehensive analysis of molecular signatures of dengue disease progression and will help unravel mechanisms of dengue disease progression. Our analysis resulted in the identification of markers that may be useful for early prediction of DHF during the febrile phase. The combination of highly sensitive analytical methods and novel statistical approaches described here forms a robust platform for biomarker discovery.
The origin of clonal diversity and structure of Populus alba in Sardinia: evidence from nuclear and plastid microsatellite markers.

BACKGROUND AND AIMS Populus alba is a thermophilic forest tree present in the Mediterranean basin. Its habitat is highly fragmented and its distribution range has been subject to long-term human interference, resulting in debate surrounding whether certain populations are native or exotic in origin. In particular, populations from the islands of Corsica and Sardinia are of uncertain origin. While populations of P. alba mainly reproduce sexually, clonal reproduction is also common. The aims of this study were to locate and molecularly characterize the poorly studied island populations of P. alba and compare these with samples from various spatial scales, in order to provide information on the genetic structure and phylogeography of this species. This information will provide evidence on whether the species is native to Sardinia, which is important for the development of conservation strategies. METHODS DNA extracts were obtained from the following P. alba trees: 159 from Sardinia, 47 from Ticino regional park (northern Italy), 15 acquired from an Italian Germoplasm Bank (IRC; Italian Reference Collection) and 28 from the Mediterranean basin (MB). Genetic polymorphisms were revealed at nuclear and chloroplast DNA (cpDNA) microsatellite loci, both at the island scale (Sardinia) and at broader scales, for comparative assessment of the genetic and genotypic diversity and phylogeography. KEY RESULTS Based on nuclear microsatellite loci, Sardinian white poplar consists of a small number of genets (26), each of which is represented by several ramets. Despite the uniqueness of the Sardinian haplotypes and the very low value of genetic diversity at the cpDNA level (vK = 0.15), the HT (0.60) and the AR (3.61) values, estimated at the nuclear level for Sardinia, were comparable with those of the other populations and collections. CONCLUSIONS The uniqueness of the cpDNA haplotypes, the prevalence of clonality and the restricted number of genets recorded suggest that Sardinian white poplar could be a floristic relict of the native flora of the island, which has spread through available habitats on the island mainly by means of vegetative propagation and human activities.
Herschel : the first science highlights Special feature L etter to the E ditor First detection of the methylidyne cation ( CH + ) fundamental rotational line with the Herschel / SPIRE FTS

Aims. To follow the species chemistry arising in diverse sources of the Galaxy with Herschel. Methods. SPIRE FTS sparse sampled maps of the Orion bar & compact HII regions G29.96-0.02 and G32.80+0.19 have been analyzed. Results. Beyond the wealth of atomic and molecular lines detected in the high-resolution spectra obtained with the FTS of SPIRE in the Orion Bar, one emission line is found to lie at the position of the fundamental rotational transition of CH as measured precisely in the laboratory by Pearson and Drouion. This coincidence suggests that it is the first detection of the fundamental rotational transition of CH. This claim is strengthened by the observation of the lambda doublet transitions arising from its relative, CH, which are also observed in the same spectrum. The broad spectral coverage of the SPIRE FTS allows for the simultaneous measurement of these closely related chemically species, under the same observing conditions. The importance of these lines are discussed and a comparison with results obtained from models of the photon dominated region (PDR) of Orion are presented. The CH line also appears in absorption in the spectra of the two galactic compact HII regions G29.96-0.02 and G32.80+0.19, which is likely due to the presence of CH in the the cold neutral medium of the galactic plane. These detections will shed light on the formation processes and on the existence of CH, which are still outstanding questions in astrophysics.
Divergent Functions Through Alternative Splicing: The Drosophila CRMP Gene in Pyrimidine Metabolism, Brain, and Behavior

DHP and CRMP proteins comprise a family of structurally similar proteins that perform divergent functions, DHP in pyrimidine catabolism in most organisms and CRMP in neuronal dynamics in animals. In vertebrates, one DHP and five CRMP proteins are products of six genes; however, Drosophila melanogaster has a single CRMP gene that encodes one DHP and one CRMP protein through tissue-specific, alternative splicing of a pair of paralogous exons. The proteins derived from the fly gene are identical over 90% of their lengths, suggesting that unique, novel functions of these proteins derive from the segment corresponding to the paralogous exons. Functional homologies of the Drosophila and mammalian CRMP proteins are revealed by several types of evidence. Loss-of-function CRMP mutation modifies both Ras and Rac misexpression phenotypes during fly eye development in a manner that is consistent with the roles of CRMP in Ras and Rac signaling pathways in mammalian neurons. In both mice and flies, CRMP mutation impairs learning and memory. CRMP mutant flies are defective in circadian activity rhythm. Thus, DHP and CRMP proteins are derived by different processes in flies (tissue-specific, alternative splicing of paralogous exons of a single gene) and vertebrates (tissue-specific expression of different genes), indicating that diverse genetic mechanisms have mediated the evolution of this protein family in animals.
Intravascular Ultrasound Findings of Early Stent Thrombosis After Primary Percutaneous Intervention in Acute Myocardial Infarction: A Harmonizing Outcomes With Revascularization and Stents in Acute Myocardial Infarction (HORIZONS-AMI) Substudy

Background— Small stent area and residual inflow/outflow disease have been reported as the strongest intravascular ultrasound (IVUS) predictors of early stent thrombosis (ST) in patients with stable angina. IVUS predictors of early ST in patients with acute myocardial infarction have not been studied. Methods and Results— In the Harmonizing Outcomes with Revascularization and Stents in Acute Myocardial Infarction (HORIZONS-AMI) study, a formal substudy included poststent and 13-month follow-up IVUS at 36 centers. Twelve patients with baseline IVUS who had definite/probable early ST ⩽30 days after enrollment were compared with 389 patients without early ST. Significant residual stenosis was a lumen area <4.0 mm2 with ≥70% plaque burden ⩽10 mm from each stent edge. Significant edge dissection was more than medial dissection with lumen area <4 mm2 or dissection angle ≥60°. Randomization to bivalirudin (P=0.29) or paclitaxel-eluting stent (P=0.74) was not related to early ST. Minimum lumen area was smaller in patients with versus without early ST (4.4 mm2 [3.6, 6.9] versus 6.7 mm2 [5.3, 8.0], respectively, P=0.014). Minimum lumen area <5 mm2, significant residual stenosis, significant stent edge dissection, and significant tissue (plaque/thrombus) protrusion (more than the median that narrowed the lumen to <4 mm2) were more prevalent in patients with early ST, but significant acute malapposition (more than the median) was not. Overall, 100% of patients with early ST had at least 1 of these significant features: minimum lumen area <5 mm2, edge dissection, residual stenosis, or tissue protrusion versus 23% in patients without early ST (P<0.01). Conclusions— Smaller final lumen area and inflow/outflow disease (residual stenosis or dissection) but not acute malapposition were related to early ST after acute myocardial infarction intervention. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00433966.
Stark-selected beam of ground-state OCS molecules characterized by revivals of impulsive alignment.

We make use of an inhomogeneous electrostatic dipole field to impart a quantum-state-dependent deflection to a pulsed beam of OCS molecules, and show that those molecules residing in the absolute ground state, X(1)Σ(+), |00(0)0>, J = 0, can be separated out by selecting the most deflected part of the molecular beam. Past the deflector, we irradiate the molecular beam by a linearly polarized pulsed nonresonant laser beam that impulsively aligns the OCS molecules. Their alignment, monitored via velocity-map imaging, is measured as a function of time, and the time dependence of the alignment is used to determine the quantum state composition of the beam. We find significant enhancements of the alignment ( = 0.84) and of state purity (>92%) for a state-selected, deflected beam compared with an undeflected beam.
Water Wave Refraction and Diffraction over Frictional Topography

- This paper considers the effects of wave energy dissipation induced by sea-bottom friction on the computational results of water wave refraction and diffraction with the parabolic equation method. The presented results show that the friction factor formula adopted in this paper is of higher numerical accuracy than that introduced by Dalrymphe (1984), and it can be used to compute wave propagation over large open areas.
AGE AND SEX DIFFERENTIALLY AFFECT REGIONAL CHANGES IN ONE REPETITION MAXIMUM STRENGTH

To assess the influences of age and sex on regional changes in 1 repetition maximum (1RM) strength, 10 young men (20–30 years), 8 young women (20–30 years), 11 older men (65–75 years), and 10 older women (65–75 years) were studied before and after a 24-week whole-body strength training program. Changes in 1RM strength were analyzed for each individual exercise, as well as by calculating a total body score (TBS), an upper body score (UBS), and a lower body score (LBS). The effect of age and sex on changes in 1RM strength was analyzed using a repeated measures analysis of variance. When changes in strength for individual exercises were analyzed, the chest press, lat pulldown, shoulder press, and triceps pushdown were affected by both age (p > 0.05) and sex (p > 0.05), while the biceps curls were only influenced by age (p > 0.05). For the lower body, the leg press changes in 1RM strength were influenced by age (p > 0.0001), while leg extension was influenced by sex (p > 0.05). Total body score, UBS, and LBS showed significant increases with 24 weeks of ST (p > 0.001, all). Changes in TBS and UBS were affected by age (p > 0.001, both) and sex (p > 0.05 and p > 0.001, respectively). Younger subjects showed a greater increase in strength than older subjects, and men showed a greater increase in strength compared with women. Changes in LBS were affected by age (p > 0.001), with younger subjects showing a greater increase in strength compared with the older subjects, but not by sex (p = 0.464). These data indicate that regional increases in strength are differentially affected by age and sex.
Parasitisme d’Apis mellifera adansonii (Latreille 1804) et de Meliponula bocandei (Spinola 1853) par Aethina tumida (Murray 1867): premier recensement au Gabon et impact sur la domestication

Le petit coleoptere des ruches, Aethina tumida (Murray 1867), a ete signale dans de nombreux pays d’Afrique subsaharienne. Ce parasite est considere comme une menace mineure pour les colonies importantes d’Apis mellifera (Linnaeus 1758) en Afrique mais une menace majeure lors du transfert des colonies sauvages de Meliponula bocandei (Spinola 1853) dans des ruches. Aucune donnee n’a ete publiee sur la situation du Gabon et la situation des colonies sauvages est mal connue. Aussi, la presente etude a pour objet : (1) de faire un premier etat de la prevalence d’A. tumida dans les colonies sauvages d’A. mellifera et M. bocandei au Gabon ; (2) de verifier l’efficacite de la mise en place d’une quarantaine lors du transfert de M. bocandei dans une ruche contre A. tumida. Ainsi, 59 nids d’A. mellifera et 25 nids de M. bocandei ont ete inspectes dans deux localites. Aussi, douze colonies de M. bocandei ont ete transferees dans des ruches avec une quarantaine de 4 jours et douze ont ete transferees sans quarantaine. Aethina tumida a ete observe dans plus de 70 % des colonies d’A. mellifera inspectees et dans une seule colonie de M. bocandei. Aucun degât n’a ete observe dans les colonies d’A. mellifera. Plus de 60 % des couvains de M. bocandei, mis en quarantaine ou non, ont ete detruits par A. tumida lors du transfert dans des ruches. Cette etude met en evidence la presence d’A. tumida au Gabon et la necessite de developper une methode de domestication plus efficace de M. bocandei dans des ruches.
Integrated Behavior of Artificial Skin

This paper deals with a system of planary distributed transducers called "Artificial skin. " The material used for this purpose is soft, homogeneous and elastic. The Belgrade hand prosthesis is covered with it. The aim of this paper is to find those properties of the sensor unit which would enable the optimal integrated behavior of the whole system to be obtained. Two basic integral properties of artificial skin are implemented: tactile perception and perception proportional to pressure on the skin. From this it is possible to have slipping perception of the grasped objects.
Towards Patient-Related Information Needs

The quality of health care depends, among others, on the quality of a physician's domain knowledge. Since it is impossible to keep up with all new findings and developments, physicians usually have gaps in their domain knowledge. To handle exceptional cases, access to the full range of medical literature is required. The specific literature needed for appropriate treatment of the patient is described by a physician's information need. Physicians are often unaware of their information needs. To support them, this paperThis research is part of the MIA project (Medical Information Agent), which is funded by NWO (grant number 634.000.021). aims at presenting a first step towards automatically formulating patient-related information needs. We start investigating how we can model a physician's information needs in general. Then we propose an approach to instantiate the model into a representation of a physician's information needs using the patient data as stored in a medical record. Our experiments show that this approach is feasible. Since the number of formulated patient-related information needs is rather high, we propose the use of filters. Future research will focus on the combination of personalization and filtering. It is expected that the resultant set of information needs will have a manageable size and contributes to the quality of health care.
Revisiting keratoconus diagnosis and progression classification based on evaluation of corneal asymmetry indices, derived from Scheimpflug imaging in keratoconic and suspect cases

Purpose To survey the standard keratoconus grading scale (Pentacam®-derived Amsler–Krumeich stages) compared to corneal irregularity indices and best spectacle-corrected distance visual acuity (CDVA). Patients and methods Two-hundred and twelve keratoconus cases were evaluated for keratoconus grading, anterior surface irregularity indices (measured by Pentacam imaging), and subjective refraction (measured by CDVA). The correlations between CDVA, keratometry, and the Scheimpflug keratoconus grading and the seven anterior surface Pentacam-derived topometric indices – index of surface variance, index of vertical asymmetry, keratoconus index, central keratoconus index, index of height asymmetry, index of height decentration, and index of minimum radius of curvature – were analyzed using paired two-tailed t-tests, coefficient of determination (r2), and trendline linearity. Results The average ± standard deviation CDVA (expressed decimally) was 0.626 ± 0.244 for all eyes (range 0.10–1.00). The average flat meridian keratometry was (K1) 46.7 ± 5.89 D; the average steep keratometry (K2) was 51.05 ± 6.59 D. The index of surface variance and the index of height decentration had the strongest correlation with topographic keratoconus grading (P < 0.001). CDVA and keratometry correlated poorly with keratoconus severity. Conclusion It is reported here for the first time that the index of surface variance and the index of height decentration may be the most sensitive and specific criteria in the diagnosis, progression, and surgical follow-up of keratoconus. The classification proposed herein may present a novel benchmark in clinical work and future studies.
Security Issues in a Synchronous e-Training Platform

Synchronous e-training is emerging as an alternative for developing human resources training plans in large organizations. Real-time communications are used to emulate face-to-face interaction that occurs in on-campus learning environments. However, the security concerns that a synchronous e-training platform must face may compromise the integrity, availability and confidentiality of corporate information, which may lead to serious economic and legal consequences. The disclosure of corporate information or the unauthorized participation in e-training activities must be prevented. In this paper, the security issues in synchronous e-training are identified, and the threats to a real e-training platform are analyzed. The platform is organized into four virtual networks with different security requirements and vulnerabilities. The platform assumes that multicast communications are available in the underlying corporate network. The threats affecting each element of the platform and their impact on e-training activities are discussed. Finally, a security scheme is proposed fixing the aforementioned vulnerabilities. Digital certificates and encryption algorithms solve most of the vulnerabilities, but other techniques such as access control lists and user skills on security basics are essential. Most of the proposed scheme is applicable to other real-time communication systems, since the e-training platform is built using standard technologies commonly used in voice over IP systems.