Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeficiency Virus Type 1

ABSTRACT Human immunodeficiency virus (HIV) infects different organs and tissues. During these infection events, subpopulations of HIV type 1 (HIV-1) develop and, if viral trafficking is restricted between subpopulations, the viruses can follow independent evolutionary histories, i.e., become compartmentalized. This phenomenon is usually detected via comparative sequence analysis and has been reported for viruses isolated from the central nervous system (CNS) and the genital tract. Several approaches have been proposed to study the compartmentalization of HIV sequences, but to date, no rigorous comparison of the most commonly employed methods has been made. In this study, we systematically compared inferences made by six different methods for detecting compartmentalization based on three data sets: (i) a sample of 45 patients with sequences gathered from the CNS, (ii) sequences from the female genital tract of 18 patients, and (iii) a set of simulated sequences. We found that different methods often reached contradictory conclusions. Methods based on the topology of a phylogenetic tree derived from clonal sequences were generally more sensitive in detecting compartmentalization than those that relied solely upon pairwise genetic distances between sequences. However, as the branching structure in a phylogenetic tree is often uncertain, especially for short, low-diversity, or recombinant sequences, tree-based approaches may need to be modified to take phylogenetic uncertainty into account. Given the frequently discordant predictions of different methods and the strengths and weaknesses of each particular methodology, we recommend that a suite of several approaches be used for reliable inference of compartmentalized population structure.
Embolic implications of combined risk factors in patients with patent foramen ovale (the CARPE criteria): consideration for primary prevention closure?

BACKGROUND Large patent foramen ovale (PFO), spontaneous right-to-left shunt, large atrial septal aneurysm (ASA), coagulation abnormalities, and prominent eustachian valve (EV) have all been independently suggested as risk factors for recurrent stroke. We sought to retrospectively evaluate risk of stroke and impact of transcatheter PFO closure in patients with concurrent large PFO, spontaneous right-to-left shunt, large ASA, coagulation abnormalities, and prominent EV. METHODS Between March 2006 and October 2008, 36 (mean age 44 +/- 10.9 years, 28 females) out of 120 consecutive patients referred to our center for transcatheter PFO closure had concomitant diagnosis of (a) large PFO on transcranial Doppler (TCD) and transesophageal echocardiography (TEE), (b) spontaneous right-to-left shunt on TCD, (c) large ASA, (d) prominent EV, and (e) coagulation abnormalities. All patients fulfilled the standard current indications for transcatheter closure and underwent preoperative TEE and brain magnetic resonance imaging (MRI), with subsequent intracardiac echocardiographic-guided transcatheter PFO closure. RESULTS Compared to the remaining PFO population in the same period, patients with all five concomitant features had more ischemic brain lesions on MRI, previous history of recurrent stroke, more frequently a history of venous thromboembolism, and more severe migraine with aura. The concomitance of all the features confers the highest risk of recurrent stroke (OR 9.9, 3.0-18 [95% CI], P < 0.001). CONCLUSIONS Despite its small sample size and nonrandomized retrospective nature, this is the first study to suggest that patients with concurrence of all the investigated characteristics have potentially a higher risk of stroke compared to controls. We thus propose the CARP criteria as a basis for further larger, longitudinal studies to assess the potential benefits of transcatheter closure in this patient subset in the absence of clinical recurrent stroke.
The role of SMARCB1/INI1 in the development of rhabdoid tumors

Rhabdoid tumors are especially lethal cancers that predominantly strike young children. The vast majority of rhabdoid tumors contain bi-allelic inactivating mutations in the SMARCB1 gene. Here we review clinicopathologic features of rhabdoid tumors and present recent insights into the mechanisms that drive oncogenesis in the absence of SMARCB1 function.
Comparison of the efficiency of evolutionary change‐based and side chain orientation‐based fold recognition potentials

The present article describes residue level knowledge based potential SORDIS. SORDIS incorporates the information on side‐chain orientation in relation to hydrophobic core centres, distance of residue from the globule centre and secondary structure. SORDIS has been tested and compared with widespread evolutionary change‐based substitution matrices (BLOSUM, PAM, GONNET, Johnson‐Overington, BLAJ, HSDM, and STROMA) in fold recognition experiments within the zone of weak sequence similarity (<16%). The obtained results show that the lower is the amino acid similarity between homologous pairs the higher is the performance of SORDIS in comparison with the potentials, based on the information about the evolutionary changes. Therefore, we propose that the employment of SORDIS in fold recognition can be useful. Proteins 2008. © 2008 Wiley‐Liss, Inc.
- 1-Benchmarking dexterous dual-arm / hand robotic manipulation

DEXMART is a European large-scale integrating project (IP) funded in the Seventh Framework Programme. The acronym stands for DEXterous and autonomous dual-arm/hand robotic manipulation with sMART sensory-motor skills: A bridge from natural to artificial cognition. The project is focused on artificial systems reproducing smart sensory-motor human skills, which operate in unstructured real-world environments. The emphasis is on manipulation capabilities achieved by dexterous and autonomous, and also human aware dual arm/hand robotic systems. The challenge is to allow a dual-arm robot including two multi-fingered redundant hands to grasp and manipulate the same objects used by human beings. The objects shall be allowed to have different shape, dimension, and weight.
Generation of Aptamers with an Expanded Chemical Repertoire

The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved or hitherto unknown properties. In this review, we discuss the nature of the functionalities appended to nucleoside triphosphates and their impact on selection experiments. The properties of the resulting modified aptamers will be described, particularly those integrated in the fields of biomolecular diagnostics, therapeutics, and in the expansion of genetic systems (XNAs).
Ethanol exposure during pregnancy persistently attenuates cranially directed blood flow in the developing fetus: evidence from ultrasound imaging in a murine second trimester equivalent model.

BACKGROUND Ethanol (EtOH) consumption during pregnancy can lead to fetal growth retardation, mental retardation, and neurodevelopmental delay. The fetal brain initiates neurogenesis and vasculogenesis during the second trimester, and depends on maternal-fetal circulation for nutrition and growth signals. We used high-resolution in vivo ultrasound imaging to test the hypothesis that EtOH interferes with fetal brain-directed blood flow during this critical developmental period. METHODS Pregnant mice were lightly anesthetized on gestational day 12 with an isoflurane/oxygen mixture. We assessed the effect of single and repeated binge-like maternal EtOH exposures at 3 g/kg, administered by intragastric gavage or intraperitoneal injection, on maternal circulation and fetal umbilical, aortic, internal carotid, and middle cerebral arterial circulation. RESULTS Binge maternal EtOH exposure, regardless of exposure route, significantly reduced fetal arterial blood acceleration and velocity time integral (VTI), from umbilical to cerebral arteries, without a change in fetal heart rate and resistivity indices. Importantly a single maternal binge EtOH exposure induced persistent suppression of fetal arterial VTI for at least 24 hours. Repeated binge episodes resulted in a continuing and persistent suppression of fetal VTI. Qualitative assessments showed that maternal EtOH exposure induced oscillatory, nondirectional blood flow in fetal cerebral arteries. Maternal cardiac and other physiological parameters remained unaltered. CONCLUSIONS These data show that binge-type maternal EtOH exposure results in rapid and persistent loss of blood flow from the umbilical artery to the fetal brain, potentially compromising nutrition and the maternal/fetal endocrine environment during a critical period for neuron formation and angiogenesis in the maturing brain.
Atypical Intradermal Smooth Muscle Neoplasms: Clinicopathologic Analysis of 84 Cases and a Reappraisal of Cutaneous “Leiomyosarcoma”

Atypical or mitotically active dermal smooth muscle neoplasms are uncommon lesions, which are most often termed “cutaneous leiomyosarcoma,” although preexisting—mostly small—series suggest a low risk of aggressive behavior. To further investigate these tumors, 84 cases from consultation and institutional files were analyzed for pathologic and clinical characteristics. There was a striking male-to-female preponderance (4.3:1), with a mean age of 56 years (range, 6 to 82y). Nine patients had a history of malignancies (6 of the skin). Tumors measured 1.3 cm on average and were predominantly located on the trunk (32) and lower extremities (30). Histologically, all tumors were confined to the dermis or showed only very superficial, focal subcutaneous extension. The majority showed an infiltrative growth pattern with fascicles of atypical eosinophilic spindle cells ramifying between dermal collagen fibers. Primary tumors showed a mean mitotic rate of 4.7/10 high-power fields. By the Fédération Nationale des Centres de Lutte Contre le Cancer grading system, 97% of primary tumors were grade I lesions, with only 3% showing necrosis. All tumors were immunopositive for smooth muscle actin; 98% expressed desmin, 90% caldesmon, and 45% pankeratin (usually focal). Follow-up in 52 cases (mean, 51 mo) showed no metastases or tumor-related deaths. Eighteen tumors showed local recurrence at a mean interval of 43 months; 12 of the recurrent lesions showed positive margins in the primary excision and 1 showed margins <0.2 cm. Margin status was not available for the other 5 cases, which recurred locally. Recurrent tumors showed, on average, 13.7 mitoses/10 high-power fields. Of recurrences, 47% were grade I lesions, 35% were grade II, and 18% were grade III, and 28% showed necrosis. The primary excision of tumors, which later recurred, showed no difference in grade, presence of necrosis, or mitotic rate, compared with those that did not recur; there were no discernible clinical differences either. In summary, these tumors, when confined to the dermis or showing only minimal subcutaneous involvement, seem to carry no evident risk of metastasis; hence, the designation “sarcoma” is inappropriate. Margin status is the most important predictor of recurrence. On excision with clear margins, the risk of local recurrence is very low. Hence, we propose the term “atypical intradermal smooth muscle neoplasm” as being more appropriate.
Approximately counting integral flows and cell-bounded contingency tables

We consider the problem of approximately counting integral flows in a network. We show that there is an fpras based on volume estimation if all capacities are sufficiently large, generalising a result of Dyer, Kannan and Mount (1997). We apply this to approximating the number of contingency tables with prescribed cell bounds when the number of rows is constant, but the row sums, column sums and cell bounds may be arbitrary. We provide an fpras for this problem via a combination of dynamic programming and volume estimation. This generalises an algorithm of Cryan and Dyer (2002) for standard contingency tables, but the analysis here is considerably more intricate.
Propranolol and Infantile Hemangiomas Four Years Later: A Systematic Review

To systematically review the literature evaluating efficacy and adverse events of propranolol treatment for infantile hemangiomas, we searched the MEDLINE and Cochrane databases for all studies examining the response of infantile hemangiomas (IHs) to propranolol published between June 12, 2008, and June 15, 2012. Forty‐one studies with 1,264 patients were included; 74% of patients were female and approximately 30% had received other treatments before propranolol. Propranolol was initiated at a mean age of 6.6 months at a mean dose of 2.1 mg/kg/day and for a mean treatment duration of 6.4 months. The response rate for patients with IHs treated with propranolol was 98% (range 82%–100%), with response rate defined as any improvement with propranolol. Treatment response rates were comparable for studies evaluating IHs at specific sites, such as periorbital IHs. Studies that followed patients after treatment completion reported IH rebound growth in 17% of patients. There were 371 adverse events reported in 1,189 patients. The most common adverse events were changes in sleep (n = 136) and acrocyanosis (n = 61). Serious adverse events were rare, with reports of symptomatic hypotension in five patients, hypoglycemia in four, and symptomatic bradycardia in one. This systematic review of 1,264 patients treated with propranolol for IHs showed a high rate of efficacy and a low rate of serious adverse events.
Security in DVB‐RCS2

This paper presents security features in the second generation digital video broadcasting with return channel via satellite standard (DVB‐RCS2). The up‐front consideration of security, and in particular transmission security (TRANSEC), started with the development of security requirements introduced in the DVB‐RCS Next Generation (NG) Commercial Requirements and Call for Technologies. It was apparent at an early stage that no single approach or implementation would satisfy the wide range of product and security requirements to span consumer, professional and government market sectors. This led to the introduction and development of two important concepts: TRANSEC profiles, a specialization of DVB‐RCS2 system level profiles concept; and TRANSEC ‘hooks’, extension points that allow TRANSEC functionality to be added as necessary, governed by profile security requirements. The bulk of this paper outlines and describes the three TRANSEC profiles presented in the DVB‐RCS2 Lower Layer Guidelines document. Finally, the various profiles are compared and contrasted. Copyright © 2013 John Wiley & Sons, Ltd.
Biodiversity conservation and management

stract: This paper gives a brief overview of the research activities of the French Institute in the field of biodiversity conservation. First, biodiversity-related issues are set in the global context, while India's own biological profile is highlighted. Then, the importance of forest management and policies are expressed, as well as the necessity of a new strategy and action plans for sustainable conservation and management of biodiversity through an integrative approach by taking into account ecological, social, economic and institutional aspects. In the wide field of biodiversity, the French Institute's research programmes have been focusing for about four decades on species diversity and ecosystem diversity at the local (i.e. stand and community), landscape and regional levels. The Institute has been concentrating on plant ecology with a strong emphasis on trees and forests, from open woodland to dense moist evergreen forests, considering their present status as well as their long-term history. Geographically speaking, most of the studies are being carried out in the western ghats and some projects in the eastern ghats and mangroves. The biodiversity-related activities of the French Institute come under 'assessment of biodiversity' and 'monitoring the dynamics of biodiversity'. Assessment employs both ecosystem and species oriented approaches and makes comprehensive use of GIS to integrate them. The monitoring of biodiversity dynamics covers studies on land use and land cover changes, ecosystem uses and forest products, and forest dynamics itself. Although these long-term efforts have already been able to put together a sum of knowledge that can help to better define conservation strategies, more insight is now to be gained on landscape changes linked to social and economic aspects of forest use and management.
Stem Cells and Labeling for Spinal Cord Injury

Spinal cord injury (SCI) is a devastating condition that usually results in sudden and long-lasting locomotor and sensory neuron degeneration below the lesion site. During the last two decades, the search for new therapies has been revolutionized with the improved knowledge of stem cell (SC) biology. SCs therapy offers several attractive strategies for spinal cord repair. The transplantation of SCs promotes remyelination, neurite outgrowth and axonal elongation, and activates resident or transplanted progenitor cells across the lesion cavity. However, optimized growth and differentiation protocols along with reliable safety assays should be established prior to the clinical application of SCs. Additionally, the ideal method of SCs labeling for efficient cell tracking after SCI remains a challenging issue that requires further investigation. This review summarizes the current findings on the SCs-based therapeutic strategies, and compares different SCs labeling approaches for SCI.
Mandibular Range of Movement and Pain Intensity in Patients with Anterior Disc Displacement without Reduction.

OBJECTIVE Temporomandibular disorders (TMD) are the most common source of orofacial pain of a non-dental origin. The study was performed to investigate the therapeutic effect of the conventional occlusal splint therapy and the physical therapy. The hypothesis tested was that the simultaneous use of occlusal splint and physical therapy is an effective method for treatment of anterior disc displacement without reduction. MATERIALS AND METHODS Twelve patients (mean age =30.5 y) with anterior disc displacement without reduction (according to RDC/TMD and confirmed by magnetic resonance imaging) were randomly allocated into 2 groups: 6 received stabilization splint (SS) and 6 received both physical therapy and stabilization splint (SS&PT). Treatment outcomes included pain-free opening (MCO), maximum assisted opening (MAO), path of mouth opening and pain as reported on visual analogue scale (VAS). RESULTS At baseline of treatment there were no significant differences among the groups for VAS scores, as well as for the range of mandibular movement. VAS scores improved significantly over time for the SS&PT group (F=28.964, p=0.0001, effect size =0.853) and SS group (F=8.794, p=0.001, effect size =0.638). The range of mouth opening improved significantly only in the SS&PT group (MCO: F=20.971, p=0.006; MAO: F=24.014, p=0.004) (Figure 2). Changes in path of mouth opening differ significantly between the groups (p=0.040). Only 1 patient in SS&PT group still presented deviations in mouth opening after completed therapy while in the SS group deviations were present in 5 patients after completed therapy. CONCLUSION This limited study gave evidence that during the treatment period lasting for 6 months, the simultaneous use of stabilization splint and physical therapy was more efficient in reducing deviations and improving range of mouth opening than the stabilization splint used alone. Both treatment options were efficient in reducing pain in patients with anterior disc displacement without reduction. Despite of objectively diagnosed disruption of temporomandibular joint anatomy, physiological function was regained.
The price of protein: combining evolutionary and economic analysis to understand excessive energy consumption

Excessive weight gain appears, thermodynamically at least, straightforward: growing energy intake and/or falling energy expenditure create an energetic surplus, resulting in fat accumulation. The situation is, however, far more complex, with genetic, physiological, social, psychological and economic factors all implicated. Thus the causes of excessive weight gain remain difficult to disentangle. We combine two recent developments from different areas of nutrition research: the study of food prices in relation to energy content and the hypothesis that an evolved propensity to regulate protein intake more strongly than non‐protein calories exerts powerful leverage on overall energy intake. We partition the energy content of a range of common supermarket foods, and show that increasing overall energy content only modestly raises the cost of foods, largely as a result of macronutrients having very different costs. Higher food prices are associated with higher protein content and lower carbohydrate content, whereas fat content was not significantly associated with food price. We show that the differential costs of energy from protein and carbohydrates may bias consumers towards diets high in carbohydrate energy, leading them to consume excessive energy to meet their dietary protein needs. We review evidence from physiology, evolution and economics that support our suggestion.
Gabapentin inhibits central sensitization during migraine

Peripheral and central sensitizations are phenomena that occur during migraine. The role of pentin, a migraine preventive drug, on central sensitization remains unclear. In this study, a rat model of migraine was established by electrical stimulation of the trigeminal ganglion, and the an-imals were given intragastric gabapentin. Changes in amino acid content in the cerebrospinal fluid and protein kinase C membrane translocation in the spinal trigeminal nucleus were examined to clarify the mechanisms underlying the efficacy of gabapentin in the treatment of central sensitization during migraine. Electrophysiology, liquid chromatography-mass spectrometry and western blot analysis results revealed that gabapentin reduces neuronal excitability in the spinal nucleus in the trigeminal nerve, decreases excitatory amino acid content and inhibits the activation of protein ki-nase C. This provides evidence that excitatory amino acids and protein kinase C are involved in the formation and maintenance of central sensitization during migraine. Gabapentin inhibits migraine by reducing excitatory amino acid content in the cerebrospinal fluid and inhibiting protein kinase C ac-tivation.
Practical approach to experimentation in a simulation study

Simulation study of complex production facilities can be a challenging task for manufacturing engineers as it requires skills to build the models and to conduct experiments. Accurate modeling but inadequate experimentation may lead to poor decision and can be detrimental particularly when financial investment is involved. This paper proposes a practical approach to simulation experimentation in the context of simulation study of an engine assembly line. The overall aim of the study was to increase the productivity and efficiency of the line. The approach was deployed in the form of a methodology that was used to select the most feasible outcome from a series of simulation experiments, taking into account the minimum effort/investment needed to implement the improvement.