Miracle-dz/UniFAR-FTUs huggingface dataset:
Two Sides of the Same Coin: TFIIH Complexes in Transcription and DNA Repair

TFIIH is organized into a seven-subunit core associated with a three-subunit Cdk-activating kinase (CAK) module. TFIIH has roles in both transcription initiation and DNA repair. During the last 15 years, several studies have been conducted to identify the composition of the TFIIH complex involved in DNA repair. Recently, a new technique combining chromatin immunoprecipitation and western blotting resolved the hidden nature of the TFIIH complex participating in DNA repair. Following the recruitment of TFIIH to the damaged site, the CAK module is released from the core TFIIH, and the core subsequently associates with DNA repair factors. The release of the CAK is specifically driven by the recruitment of the DNA repair factor XPA and is required to promote the incision/excision of the damaged DNA. Once the DNA lesions have been repaired, the CAK module returns to the core TFIIH on the chromatin, together with the release of the repair factors. These data highlight the dynamic composition of a fundamental cellular factor that adapts its subunit composition to the cell needs.
Nonlinear registration using B-spline feature approximation and image similarity

The warping methods are broadly classified into the image-matching method based on similar pixel intensity distribution and the feature-matching method using distinct anatomical feature. Feature based methods may fail to match local variation of two images. However, the method globally matches features well. False matches corresponding to local minima of the underlying energy functions can be obtained through the similarity based methods. To avoid local minima problem, we proposes non-linear deformable registration method utilizing global information of feature matching and the local information of image matching. To define the feature, gray matter and white matter of brain tissue are segmented by Fuzzy C-Mean (FCM) algorithm. B-spline approximation technique is used for feature matching. We use a multi-resolution B-spline approximation method which modifies multilevel B-spline interpolation method. It locally changes the resolution of the control lattice in proportion to the distance between features of two images. Mutual information is used for similarity measure. The deformation fields are locally refined until maximize the similarity. In two 3D T1 weighted MRI test, this method maintained the accuracy by conventional image matching methods without the local minimum problem.
Running Head : fMRI of rCBF in RA Brain Correlates of Continuous Pain in Rheumatoid Arthritis as Measured by Pulsed Arterial Spin Labeling

Objective: Central nervous system pathways involving pain modulation shape the pain experience in patients with chronic pain. Our objectives were to understand the mechanisms underlying pain in rheumatoid arthritis (RA) and identify brain signals that may serve as imaging markers for developing targeted treatments for RA pain. Methods: Subjects with RA and matched controls underwent functional magnetic resonance imaging, using pulsed arterial spin labeling (pASL). The imaging conditions included: 1) resting state, 2) low intensity stimulus and 3) high intensity stimulus. Stimuli consisted of mechanical pressure applied to metacarpophalangeal (MCP) joints with an automated cuff inflator. The low intensity stimulus was 30 mmHg. The high intensity stimulus was the amount of pressure required to achieve 40/100 pain intensity for each RA patient, with the same amount of pressure given to the matched control. A cc ep te d A rt ic le This article is protected by copyright. All rights reserved. Results: Among RA patients, regional cerebral blood flow (rCBF) in medial frontal cortex (MFC) and dorsolateral prefrontal cortex increased during both low and high pressure stimuli. No rCBF changes were noted for pain-free controls. In region of interest analyses among RA patients, baseline rCBF in MFC was negatively correlated with pressure required for the high intensity stimulus (p<0.01) and positively correlated with pain induced by the low intensity stimulus (p<0.05). Baseline rCBF also marginally correlated with disease activity (p=0.05). rCBF during high pain was positively correlated with pain severity and interference (p’s<0.05). Conclusion: In response to clinically-relevant joint pain evoked by MCP pressure, neural processing in MFC increases and is directly associated with clinical pain in RA. SIGNIFICANCE AND INNOVATION • This study is the first to identify the medial frontal cortex (MFC) as a key area involved in the sensation and/or regulation of tonic, clinically-relevant joint pain in rheumatoid arthritis (RA). • Joint pain exacerbation was associated with increases in regional cerebral blood flow (rCBF) in the MFC, and rCBF in the MFC was significantly associated with pain severity and interference. • The results from this study will inform the development of targeted pharmacologic and non-pharmacologic interventions for pain in systemic inflammatory conditions, such as RA.
Do Higher Salaries Yield Better Teachers and Better Student Outcomes?

We study the effects of a policy aimed at attracting experienced teachers in primary schools in disadvantaged neighborhoods in Uruguay. Teachers in these schools could earn higher salaries. Program eligibility was based on a poverty index with a cutoff rule. Estimates from regression discontinuity models show that the policy increased teacher experience. Overall, the effect on student outcomes was small. The program may have increased experience in ways that are not strongly associated with improved student outcomes. Consistent with this, we do find achievement gains for students in schools that saw a reduction in the share of very inexperienced teachers.
Immediate Implant Placement by Interradicular Bone Drilling before Molar Extraction: Clinical Case Report with One-Year Follow-Up

The placement of immediate implants in the posterior sector is a widespread procedure where the success and survival rates are similar to those of traditional protocols. It has several anatomical challenges, such as the presence of interradicular bone septa that hinder a correct three-dimensional positioning of the implant and may compromise primary stability and/or cause damage of neighboring structures. The aim of this article is to present the treatment and the one-year clinical follow-up of a patient who received immediate implant placement using an interradicular bone-drilling technique before the molar extraction.
Determination of Chlortetracycline Residues, Antimicrobial Activity and Presence of Resistance Genes in Droppings of Experimentally Treated Broiler Chickens

Tetracyclines are important antimicrobial drugs for poultry farming that are actively excreted via feces and urine. Droppings are one of the main components in broiler bedding, which is commonly used as an organic fertilizer. Therefore, bedding becomes an unintended carrier of antimicrobial residues into the environment and may pose a highly significant threat to public health. For this depletion study, 60 broiler chickens were treated with 20% chlortetracycline (CTC) under therapeutic conditions. Concentrations of CTC and 4-epi-CTC were then determined in their droppings. Additionally, this work also aimed to detect the antimicrobial activity of these droppings and the phenotypic susceptibility to tetracycline in E. coli isolates, as well as the presence of tet(A), tet(B), and tet(G) resistance genes. CTC and 4-epi-CTC concentrations that were found ranged from 179.5 to 665.8 µg/kg. Based on these data, the depletion time for chicken droppings was calculated and set at 69 days. All samples presented antimicrobial activity, and a resistance to tetracyclines was found in bacterial strains that were isolated from these samples. Resistance genes tet(A) and tet(B) were also found in these samples.
Possible connection of short posterior ciliary arteries to choroidal neovascularisations in eyes with pathologic myopia

Purpose To determine the connection between myopic choroidal neovascularisations (CNVs) and intrascleral vessels examined by swept-source optical coherence tomography (OCT). Methods The data of 124 eyes of 112 consecutive patients with myopic CNVs were retrospectively analysed. A myopic CNV was defined as a CNV occurring in eyes with pathologic myopia based on the META-PM study classification. The images obtained by swept-source OCT were analysed to determine the relationship between perforating scleral vessels and CNVs. The continuity of the scleral vessels and the CNV was also analysed. The OCT angiographic (OCTA) characteristics of the myopic CNVs at the active, scar and atrophic phases were also analysed. Results OCTA images showed that CNVs had blood flow in the active, scar and atrophic phases. Scleral perforating vessels were detected just below or around the CNV in 93 eyes (75%). In 10 of the 93 eyes, the scleral vessels and CNV appeared to be continuous through a defect of Bruch’s membrane in the OCT images. Indocyanine green angiography showed that these perforating vessels were intrascleral arteries originating from the short posterior ciliary arteries (SPCAs). Conclusions Swept-source OCT showed that some of the myopic CNVs were continuous with scleral vessels mainly the SPCA. Further studies to confirm angiographical continuity between these two components are necessary.
Dynamicity and Durability in Scalable Visual Instance Search

Visual instance search involves retrieving from a collection of images the ones that contain an instance of a visual query. Systems designed for visual instance search face the major challenge of scalability: a collection of a few million images used for instance search typically creates a few billion features that must be indexed. Furthermore, as real image collections grow rapidly, systems must also provide dynamicity, i.e., be able to handle on-line insertions while concurrently serving retrieval operations. Durability, which is the ability to recover correctly from software and hardware crashes, is the natural complement of dynamicity. Durability, however, has rarely been integrated within scalable and dynamic high-dimensional indexing solutions. This article addresses the issue of dynamicity and durability for scalable indexing of very large and rapidly growing collections of local features for instance retrieval. By extending the NV-tree, a scalable disk-based high-dimensional index, we show how to implement the ACID properties of transactions which ensure both dynamicity and durability. We present a detailed performance evaluation of the transactional NV-tree: (i) We show that the insertion throughput is excellent despite the overhead for enforcing the ACID properties; (ii) We also show that this transactional index is truly scalable using a standard image benchmark embedded in collections of up to 28.5 billion high-dimensional vectors; the largest single-server evaluations reported in the literature.
urgical treatment of thoracic spine fractures . Outcomes on 50 atients at 23 months follow-up

Purpose: The morphological and biomechanical features of the thoracic spine, together with its close proximity to the spinal cord, set it apart from other spinal segments. Management of thoracic spine injuries consists of achieving a reduction and an immediate and long-lasting stabilization of the spine while constantly protecting the central and peripheral nervous system. The aim of this study was to determine the best treatment for surgical thoracic spine fractures. Materials and methods: We studied the baseline characteristics of 68 patients admitted to our neurosurgical department for one or several thoracic spine fractures between 2008 and 2010. We analysed on this group of patient the surgical management, complications and functional outcomes. We detailed the 2-years radiological outcome on 50 patients (23 months mean follow-up). Results: The majority of patients underwent an extensive posterior arthrodesis bridging, on average, 5.3 vertebrae. The median time between diagnosis and surgery was 2 days and the median length of stay in hospital was 13.5 days. About 94% of hooks and 80% of pedicle screws were considered stable. Mean values of reduction and correction loss were similar (about 4.5◦). We concluded to the superiority of extensive procedures and of pedicle screws fixation for the reduction and the maintenance of the correction by the end of follow-up. Functional data indicated daily discomfort and moderate pain. Conclusion: A prospective study comparing the different procedures and instrumentations is needed to better define guidelines for the management of thoracic spine injuries. Level of evidence: Level IV. © 2014 Elsevier Masson SAS. All rights reserved.
Cytotoxic Activity of Extracts from Plants of Central Argentina on Sensitive and Multidrug-Resistant Leukemia Cells: Isolation of an Active Principle from Gaillardia megapotamica

Plants are a significant reservoir of cytotoxic agents, including compounds with the ability to interfere with multidrug-resistant (MDR) cells. With the aim of finding promising candidates for chemotherapy, 91 native and naturalized plants collected from the central region of Argentina were screened for their cytotoxic effect toward sensitive and MDR P-glycoprotein (P-gp) overexpressing human leukemia cells by means of MTT assays. The ethanol extracts obtained from Aldama tucumanensis, Ambrosia elatior, Baccharis artemisioides, Baccharis coridifolia, Dimerostemma aspilioides, Gaillardia megapotamica, and Vernonanthura nudiflora presented outstanding antiproliferative activity at 50 μg/mL, with inhibitory values from 93 to 100%, when tested on the acute lymphoblastic leukemia (ALL) cell line CCRF-CEM and the resistant derivative CEM-ADR5000, while 70–90% inhibition was observed against the chronic myelogenous leukemia (CML) cell K562 and its corresponding resistant subline, Lucena 1. Subsequent investigation showed these extracts to possess marked cytotoxicity with IC50 values ranging from 0.37 to 29.44 μg/mL, with most of them being below 7 μg/mL and with ALL cells, including the drug-resistant phenotype, being the most affected. G. megapotamica extract found to be one of the most effective and bioguided fractionation yielded helenalin (1). The sesquiterpene lactone displayed IC50 values of 0.63, 0.19, 0.74, and 0.16 μg/mL against K562, CCRF-CEM, Lucena 1, and CEM/ADR5000, respectively. These results support the potential of these extracts as a source of compounds for treating sensitive and multidrug-resistant leukemia cells and support compound 1 as a lead for developing effective anticancer agents.
Laboratory evaluation of a few plant extracts for their ovicidal, larvicidal and pupicidal activity against medically important human dengue, chikungunya and Zika virus vector, Aedes aegypti Linnaeus 1762 (Diptera: Culicidae)

Vector control is by far the most successful method for reducing incidences of mosquito-borne diseases. Plant products have been tested as insecticides against mosquitoes as they are nontoxic to mammals and are promising candidates to replace conventional insecticides. In the present study, the bioefficacy of crude solvent leaf extracts of Alternanthera sessilis (Amaranthaceae), Amaranthus dubius (Amaranthaceae), Sesbania grandiflora (Fabaceae) and Solanum nigrum (Solanaceae) were tested on the immature stages of the dengue, chikungunya, yellow fever and Zika virus vector, Aedes aegypti. The eggs, larvae and pupae of Aedes aegypti were exposed to different concentrations viz., 62.5, 125, 250 and 500mg/L. After 24 hours of exposure, the larval and pupal per cent mortality was assessed and their LC50 and LC90 values calculated. However, per cent egg mortality was calculated after 72 hours of exposure. Among the different crude solvent extracts of the plants tested, the butanol extract of Alternanthera sessilis caused highest egg mortality rate of 86% and the ethanol extract of Solanum nigrum exhibited highest larvicidal and pupicidal activity and LC50 and LC90 values were 34.12, 88.11 and 44.15, 111.70mg/L respectively. The successful results of preliminary studies on mosquitocidal potential of plant extracts encourage further effort to investigate the bioactive compounds in those extracts that might possess good immature mosquitocidal properties when isolated in pure form.
Hierarchical renormalization-group study on the planar bond-percolation problem

For certain hierarchical structures, one can study the percolation problem using the renormalization-group method in a very precise way. We show that the idea can also be applied to two-dimensional planar lattices by regarding them as hierarchical structures. Either a lower bound or an exact critical probability can be obtained using this method and the correlation-length critical exponent is approximately estimated as ν≈1.
MACS – a new SPM toolbox for model assessment, comparison and selection

Background In cognitive neuroscience, functional magnetic resonance imaging (fMRI) data are widely analyzed using general linear models (GLMs). However, model quality of GLMs for fMRI is rarely assessed, in part due to the lack of formal measures for statistical model inference. New Method We introduce a new SPM toolbox for model assessment, comparison and selection (MACS) of GLMs applied to fMRI data. MACS includes classical, information-theoretic and Bayesian methods of model assessment previously applied to GLMs for fMRI as well as recent methodological developments of model selection and model averaging in fMRI data analysis. Results The toolbox – which is freely available from GitHub – directly builds on the Statistical Parametric Mapping (SPM) software package and is easy-to-use, general-purpose, modular, readable and extendable. We validate the toolbox by reproducing model selection and model averaging results from earlier publications. Comparison with Existing Methods A previous toolbox for model diagnosis in fMRI has been discontinued and other approaches to model comparison between GLMs have not been translated into reusable computational resources in the past. Conclusions Increased attention on model quality will lead to lower false-positive rates in cognitive neuroscience and increased application of the MACS toolbox will increase the reproducibility of GLM analyses and is likely to increase the replicability of fMRI studies.
Lycium barbarum Polysaccharide Supplementation Improves Alcoholic Liver Injury in Female Mice by Inhibiting Stearoyl‐CoA Desaturase 1

SCOPE Lycium barbarum polysaccharide (LBP) is a water fraction of wolfberry, which has been demonstrated to possess a hepatoprotective effect in several liver disease models. However, the anti-alcoholic liver disease (anti-ALD) mechanism of LBP has not been investigated thoroughly. Its protective effects on both male and femal mice are investigated in the current study. METHODS AND RESULTS A chronic ethanol-fed ALD in vivo model is applied to study the effect of LBP in both male and female mice. It is observed that ethanol causes more severe liver injury in female than male mice, and the ameliorative effects of LBP are also more significant in female mice, which are impaired after complete bilateral oophorectomy. The hepatic SCD1 expression is found to be positively correlated with the severity of the liver damage and the main mediator of LBP inducer of protection. The AMPK-CPT pathway is also activated by LBP to rebalance the dysregulated lipid metabolism during ALD development. By using concurrent sodium palmitate and an ethanol-induced in vitro cell damage model in AML-12 cell line, it is characterized that LBP directly interacts with ERα instead of ERβ to activate the SCD1-AMPK-CPT pathway. CONCLUSIONS LBP is an effective and safe hepatoprotective agent against ALD primarily through the SCD1-AMPK-CPT pathway after ERα agonist.
Reduction in activating transcription factor 4 promotes carbon tetrachloride and lipopolysaccharide/D‑galactosamine‑mediated liver injury in mice.

Although activating transcription factor 4 (ATF4) is involved in the regulation of numerous biological functions, whether ATF4 has a direct role in liver injury is unknown. The aim of the present study was to investigate the role of ATF4 in liver injury using mouse models. The results revealed that ATF4 protein is expressed markedly higher in the mouse liver when in comparison with other tissues. Notably, tunicamycin treatment, an endoplasmic reticulum (ER) stress inducer, induced the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α), but decreased ATF4 protein levels in the mouse liver. This suggested an unconventional regulation pattern of ATF4 protein not associated with ER stress or eIF2α. In addition, it was also observed that the liver levels of ATF4 protein were significantly reduced upon chronic liver injury induced by carbon tetrachloride (CCl4). ATF4 protein was also decreased in acute liver injury induced by lipopolysaccharide (LPS) plus D‑galactosamine (D‑GalN). Furthermore, the results revealed that knockdown of ATF4 by injecting ATF4‑targeting Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)‑CRISPR associated protein 9 plasmids exacerbated CCl4 and LPS/D‑GalN‑induced liver injury as demonstrated by elevated serum aspartate transaminase and alanine aminotransferase levels. ATF4 suppression also enhanced CCl4 and LPS/D‑GalN mediated c‑Jun N‑terminal kinase activation. By contrast, ATF4 overexpression alleviated CCl4 and LPS/D‑GalN‑induced liver injury. Taken together, these observations suggested that ATF4 may serve a protective role in the mouse liver.
A Review on Biomechanics of Anterior Cruciate Ligament and Materials for Reconstruction

The anterior cruciate ligament is one of the six ligaments in the human knee joint that provides stability during articulations. It is relatively prone to acute and chronic injuries as compared to other ligaments. Repair and self-healing of an injured anterior cruciate ligament are time-consuming processes. For personnel resuming an active sports life, surgical repair or replacement is essential. Untreated anterior cruciate ligament tear results frequently in osteoarthritis. Therefore, understanding of the biomechanics of injury and properties of the native ligament is crucial. An abridged summary of the prominent literature with a focus on key topics on kinematics and kinetics of the knee joint and various loads acting on the anterior cruciate ligament as a function of flexion angle is presented here with an emphasis on the gaps. Briefly, we also review mechanical characterization composition and anatomy of the anterior cruciate ligament as well as graft materials used for replacement/reconstruction surgeries. The key conclusions of this review are as follows: (a) the highest shear forces on the anterior cruciate ligament occur during hyperextension/low flexion angles of the knee joint; (b) the characterization of the anterior cruciate ligament at variable strain rates is critical to model a viscoelastic behavior; however, studies on human anterior cruciate ligament on variable strain rates are yet to be reported; (c) a significant disparity on maximum stress/strain pattern of the anterior cruciate ligament was observed in the earlier works; (d) nearly all synthetic grafts have been recalled from the market; and (e) bridge-enhanced repair developed by Murray is a promising technique for anterior cruciate ligament reconstruction, currently in clinical trials. It is important to note that full extension of the knee is not feasible in the case of most animals and hence the loading pattern of human ACL is different from animal models. Many of the published reviews on the ACL focus largely on animal ACL than human ACL. Further, this review article summarizes the issues with autografts and synthetic grafts used so far. Autografts (patellar tendon and hamstring tendon) remains the gold standard as nearly all synthetic grafts introduced for clinical use have been withdrawn from the market. The mechanical strength during the ligamentization of autografts is also highlighted in this work.