Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mnn2 Mannosyltransferase Family Modulates Mannoprotein Fibril Length, Immune Recognition and Virulence of Candida albicans

The fungal cell wall is the first point of interaction between an invading fungal pathogen and the host immune system. The outer layer of the cell wall is comprised of GPI anchored proteins, which are post-translationally modified by both N- and O-linked glycans. These glycans are important pathogen associated molecular patterns (PAMPs) recognised by the innate immune system. Glycan synthesis is mediated by a series of glycosyl transferases, located in the endoplasmic reticulum and Golgi apparatus. Mnn2 is responsible for the addition of the initial α1,2-mannose residue onto the α1,6-mannose backbone, forming the N-mannan outer chain branches. In Candida albicans, the MNN2 gene family is comprised of six members (MNN2, MNN21, MNN22, MNN23, MNN24 and MNN26). Using a series of single, double, triple, quintuple and sextuple mutants, we show, for the first time, that addition of α1,2-mannose is required for stabilisation of the α1,6-mannose backbone and hence regulates mannan fibril length. Sequential deletion of members of the MNN2 gene family resulted in the synthesis of lower molecular weight, less complex and more uniform N-glycans, with the sextuple mutant displaying only un-substituted α1,6-mannose. TEM images confirmed that the sextuple mutant was completely devoid of the outer mannan fibril layer, while deletion of two MNN2 orthologues resulted in short mannan fibrils. These changes in cell wall architecture correlated with decreased proinflammatory cytokine induction from monocytes and a decrease in fungal virulence in two animal models. Therefore, α1,2-mannose of N-mannan is important for both immune recognition and virulence of C. albicans.
HYDRO-THERMAL FLOW IN A ROUGH FRACTURE

Heat exchange during laminar flow is studied at the fracture scale on the basis of the Stokes equation. We used a synthetic aperture model (a self-affine model) that has been shown to be a realistic geometrical description of the fracture morphology. We developed a numerical modelling using a finite difference scheme of the hydrodynamic flow and its coupling with an advection/conduction description of the fluid heat. As a first step, temperature within the surrounding rock is supposed to be constant. Influence of the fracture roughness on the heat flux through the wall, is estimated and a thermalization length is shown to emerge. Implications for the Soultz-sous-Forêts geothermal project are discussed.
An annotated list of fish parasites (Copepoda, Monogenea, Digenea, Cestoda and Nematoda) collected f

Parasites were collected from 17 species of emperors and emperor bream (Lethrinidae) in the waters off New Caledonia, South Pacific. Host-parasite and parasite-hosts lists are provided, with a total of 188 host-parasite combinations (11 per fish species), including 81 identifications at the species level. A total of 52 parasites were identified at the species level, and 40 new host records were found. Results are presented for larval isopods, copepods (16 species), monogeneans (24), digeneans (27), cestodes (11) and nematodes (10). When results were restricted to the four best-sampled fish species for which more than 30 specimens were examined, the number of host-parasite combinations was 22.25 per fish species, and the number of parasite taxa identified at the species level was 9.5 per fish species. From these data, the total number of metazoan parasite species predicted from all lethrinid species of New Caledonia, based on a classification of fish sizes using length in three categories, is 340, i.e. 13 per fish species. A biogeographical comparison with Heron Island on the Great Barrier Reef (Queensland, Australia) was possible only for a single fish species, Lethrinus miniatus: in a total of 65 host-parasite combinations, only five taxa identified at the species level (three monogeneans and two digeneans) were shared at both localities. Parasite biodiversity in lethrinids was of similar magnitude to that in groupers (Serranidae Epinephelinae) in the same area, and this study confirms a previous prediction of 10 parasite species per coral reef fish species. Although this study required significant sampling and identification, we estimate that only 13% of the parasites of lethrinids are known in New Caledonia.
Accumulation of Protease Mutations among Patients Failing Second-Line Antiretroviral Therapy and Response to Salvage Therapy in Nigeria

Background To date, antiretroviral therapy (ART) guidelines and programs in resource-limited settings (RLS) have focused on 1st- and 2nd-line (2 L) therapy. As programs approach a decade of implementation, policy regarding access to 3rd-line (3 L) ART is needed. We aimed to examine the impact of maintaining patients on failing 2 L ART on the accumulation of protease (PR) mutations. Methods and Findings From 2004–2011, the Harvard/APIN PEPFAR Program provided ART to >100,000 people in Nigeria. Genotypic resistance testing was performed on a subset of patients experiencing 2 L failure, defined as 2 consecutive viral loads (VL)>1000 copies/mL after ≥6 months on 2 L. Of 6714 patients who received protease inhibitor (PI)-based ART, 673 (10.0%) met virologic failure criteria. Genotypes were performed on 61 samples. Patients on non-suppressive 2 L therapy for <12 months prior to genotyping had a median of 2 (IQR: 0–5) International AIDS Society (IAS) PR mutations compared with 5 (IQR: 0–6) among patients failing for >24 months. Patients developed a median of 0.6 (IQR: 0–1.4) IAS PR mutations per 6 months on failing 2 L therapy. In 38% of failing patients no PR mutations were present. For patients failing >24 months, high- or intermediate-level resistance to lopinavir and atazanavir was present in 63%, with 5% to darunavir. Conclusions This is the first report assessing the impact of duration of non-suppressive 2 L therapy on the accumulation of PR resistance in a RLS. This information provides insight into the resistance cost of failing to switch non-suppressive 2 L regimens and highlights the issue of 3 L access.
Deep Action Parsing in Videos With Large-Scale Synthesized Data

Action parsing in videos with complex scenes is an interesting but challenging task in computer vision. In this paper, we propose a generic 3D convolutional neural network in a multi-task learning manner for effective Deep Action Parsing (DAP3D-Net) in videos. Particularly, in the training phase, action localization, classification, and attributes learning can be jointly optimized on our appearance-motion data via DAP3D-Net. For an upcoming test video, we can describe each individual action in the video simultaneously as: Where the action occurs, What the action is, and How the action is performed. To well demonstrate the effectiveness of the proposed DAP3D-Net, we also contribute a new Numerous-category Aligned Synthetic Action data set, i.e., NASA, which consists of 200 000 action clips of over 300 categories and with 33 pre-defined action attributes in two hierarchical levels (i.e., low-level attributes of basic body part movements and high-level attributes related to action motion). We learn DAP3D-Net using the NASA data set and then evaluate it on our collected Human Action Understanding data set and the public THUMOS data set. Experimental results show that our approach can accurately localize, categorize, and describe multiple actions in realistic videos.
Optimum dowel spacing for corner joints in 32-mm cabinet construction

The increased utilization of European 32-mm cabinet construction in the Turkish furniture industry has highlighted the need for practical strength performance evaluation of case construction. A basic understanding of the influence of dowel spacing on comer joint strength performance in case construction is necessary to assist furniture manufacturers as they engineer their products. To date, limited research had been done. This paper presents results of evaluating the effect of dowel spacing on bending moment capacity of comer joints in 32-mm case construction. Laminated particleboard and laminated medium density fiberboard (MDF) comer joints were tested under compression and tension loads. Experiments have shown that maximum moment is obtained in joints when the spacing between dowels is at least 96 mm. Also, statistical analysis of the test data indicated that joints loaded in tension and compression had significant differences at the 5 percent significance level in moment resistance since joint strength was strongly related to the internal bond strength of the board loaded in compression. In both tension and compression tests, MDF corner joints were stronger than particleboard comer joints.
Increased Fat Absorption From Enteral Formula Through an In-line Digestive Cartridge in Patients With Cystic Fibrosis

Objectives: Supplemental enteral nutrition (EN) is used by approximately 12% of people with cystic fibrosis (CF). The objective of this study was to evaluate the safety, tolerability, and fat absorption of a new in-line digestive cartridge (Relizorb) that hydrolyzes fat in enteral formula provided to patients with CF. Methods: Patients with CF receiving EN participated in a multicenter, randomized, double-blind, crossover trial with an open-label safety evaluation period. Plasma omega-3 fatty acid (FA) concentrations were measured and used as markers of fat absorption. Gastrointestinal symptoms were recorded to evaluate safety and tolerability. Information regarding the effect of EN on appetite and breakfast consumption was also collected. Results: Before study entry, participants had received EN for a mean of 6.6 years at a mean volume of approximately 800 mL, yet had a mean body mass index of only 17.5 kg/m2 and omega-3 FA plasma concentrations were only 60% of levels found in normal healthy subjects. Compared with placebo, cartridge use resulted in a statistically significant 2.8-fold increase in plasma omega-3 FA concentrations. There were no adverse experiences associated with cartridge use, and a decrease in the frequency and severity of most symptoms of malabsorption was observed with cartridge use. Participants reported increased preservation of appetite and breakfast consumption with cartridge use compared with their pre-study regimen. Conclusions: Use of this in-line digestive cartridge was safe and well tolerated, and resulted in significantly increased levels of plasma omega-3 FA used with enteral formula, suggesting an overall increased fat absorption.
Range Use Patterns and Spatial Relationships of Merriam's Kangaroo Rats (Dipodomys Merriami)

Radiotelemetry was used to investigate the home range patterns and inter-individual spatial relationships of Merriam's kangaroo rat (Dipodomys merriami). Sixty adult D. merriami (32 males and 28 females) were radio-tracked for varying lengths of time over three study periods between November 1980 and December 1982, on two desert habitat sites located near Palm Desert, California. Analyses of home range size and utilization patterns, range overlap with conspecifics, and day burrow distribution and use patterns were carried out. Home range varied between 0.03 ha and 1.16 ha with substantial inter-study differences but no apparent sex differences. Animals maintained relatively stable core activity loci within their ranges which were centered around frequently occupied day burrows. However, long sallies of 100 m or more away from core areas were not uncommon. The examination of shifts in animals' centers-of-activity (COA) over long periods of time indicated that animals maintained relatively stable home ranges over seasons and even years although a few individuals did exhibit COA shifts of more than 100 m. There was substantial home range overlap, with individuals overlapping the ranges of up to 14 radio-implanted conspecifics. The home ranges of pairs of neighboring females overlapped less than did those of males or pairs of opposite sex, and the average nearest-neighbor distance between the day burrows of males and females was significantly smaller than the average nearest-neighbor distance between females. Thus in kangaroo rats, as in other "solitary" rodents, females maintain territorial spacing to a greater degree than do males. D. merriami utilized several day burrows with moves occurring once every four days on average. However, most animals used only one or two day burrows frequently. The largest moves coincided with reproductive activity, and in particular with the day of estrus. The findings are discussed with respect to their implications for D. merriami social structure, and for comparative studies within the genus Dipodomys and within the order Rodentia.
Effects of mean arterial pressure on cerebral perfusion during cardiopulmonary bypass: a review.

Cardiopulmonary bypass (CPB) remains an essential component of many cardiac surgical procedures. The non-physiologic nature of CPB flow creates a complex array of challenges, which can threaten optimal perfusion and patient well being. It is easy enough to assert that the per-fusionist’s responsibility is to provide enough blood flow to meet the metabolic requirements of the patient’s tissues. In practice, however, it is difficult to ensure that this condition is always being met. The essence of the problem is that we
Fabrication and Electrical and Mechanical Properties of Carbon Nanotube Interconnections

Individual carbon nanotubes (CNTs) have been cut, manipulated, and soldered via electron‐beam‐induced deposition of amorphous carbon (a‐C) and using a scanning tunneling microscope inside a transmission electron microscope. All CNT structures, including simple tube–tube connections, crossed junctions, T‐junctions, zigzag structures, and even nanotube networks, have been successfully constructed with a high degree of control, and their electrical and mechanical properties have been measured in situ inside the transmission electron microscope. It is found that multiple CNTs may be readily soldered together with moderate junction resistance and excellent mechanical resilience and strength, and the junction resistance may be further reduced by current‐induced graphitization of the deposited a‐C on the junction.
Comparative Cardiovascular Risk of Abatacept and Tumor Necrosis Factor Inhibitors in Patients With Rheumatoid Arthritis With and Without Diabetes Mellitus: A Multidatabase Cohort Study

Background We examined the cardiovascular risk of abatacept compared with tumor necrosis factor (TNF) inhibitors in patients with rheumatoid arthritis with and without diabetes mellitus (DM). Methods and Results We conducted a cohort study of patients with rheumatoid arthritis who newly started abatacept or TNF inhibitors using claims data from Medicare and MarketScan. The primary outcome was a composite cardiovascular end point of myocardial infarction (MI), stroke/transient ischemic attack, and coronary revascularization. To account for >60 baseline characteristics, abatacept initiators were 1:1 propensity score (PS) matched to TNF initiators in each database. Cox proportional hazards models estimated hazard ratio (HR) and 95% confidence interval (CI) in the PS‐matched cohort per database. A fixed‐effects meta‐analysis pooled database‐specific HRs. We included a total of 13 039 PS‐matched pairs of abatacept and TNF inhibitor initiators (6103 pairs in Medicare and 6936 pairs in MarketScan). A total of 34.7% in Medicare and 19.8% in MarketScan had baseline DM. The HR (95% CI) for the primary outcome associated with abatacept use versus TNF inhibitor was 0.81 (0.66–0.99) in Medicare and 0.95 (0.74–1.23) in MarketScan, with a pooled HR of 0.86 (95% CI, 0.73–1.01; P=0.3 for heterogeneity). The risk of the primary outcome was lower in abatacept initiators versus TNF inhibitors in the DM subgroup, with a pooled HR of 0.74 (95% CI, 0.57–0.96; P=0.7 for heterogeneity), but not in the non‐DM subgroup, with a pooled HR of 0.94 (95% CI, 0.77–1.14; P=0.4 for heterogeneity). Conclusions In this large population‐based cohort of patients with rheumatoid arthritis, abatacept use appeared to be associated with a modestly reduced cardiovascular risk when compared with TNF inhibitor use, particularly in patients with DM.
Agrowaste-based composites from cocoa pod husk and polypropylene

Cocoa pod husk (CPH)-filled polypropylene (PP) composites were prepared via melt compounding. The effect of filler content and chemical treatment using 3-mercaptopropyltrimethoxysilane (MPS) and sodium dodecyl sulfate (SDS) on properties of composites were investigated. The results indicated that the treated composites with MPS and SDS improved the tensile strength, tensile modulus, thermal stability, stabilization torque, water resistivity, and crystallinity of composites. The treated composites with SDS show better tensile properties and water resistivity than composites treated with MPS. Scanning electron microscopic results show that the interfacial bonding between CPH and PP matrix improved with the presence of MPS or SDS.
DISTORTIONAL BUCKLING OF STAINLESS STEEL SECTION

This section of research describes the experimental and numerical investigation of coldformed, thin-walledstainless steel sections subject to distortional buckling under compression. Austenitic 304,ferritic 430 stainless steel and ferritic-like 3Cr12 chromium weldable steel sheets were brakepressedinto simple-lipped channels and lipped channels with intermediate stiffeners. A full setof coupon tests reveal material nonlinearity with low proportionality stress and low n-parameter,anisotropy and yield strength enhancements up to 2.33 times due to cold-forming. experimental tests and more than 570 finite element tests covering a distortional bucklingslenderness range 0.47 ≤ λd ≤ 3.64 and corner to thickness ratios of 1 and 2.5 reveal materialnonlinearity and enhanced corner properties have the most influence on the strength andbehaviour of stainless steel sections and that material anisotropy can be ignored. Enhancedcorner properties may become significant for stocky sections, where λd <1, with a corner area ofat least 10%. Current effective width approach and direct strength methods to design fordistortional buckling of stainless steel and coldformed carbon steel available. Modified resistance factors arerecommended for the effective width approach of current design codes to meet limit statesdesign criteria. Direct strength design curves are developed for austenitic and ferriticstainlesssteel alloys for inclusion for stainless steel structures. This section of research also describes the experimental and theoretical investigation of twocommercially available wide-flange, ferritic 445 stainless steel roof sections under purebending. A total of nine tests exhibited distortional buckling behaviour withthe interaction of flange curling. The effects of flange curling and material nonlinearity wereevident as shown by the considerable loss of stiffness in the test results before reaching theultimate load. The theoretical evaluation of flange-curling deformations shows that a truerepresentation of the wide-flange support condition provided by the web is essential to obtainreasonable agreement with experimental tests. The iterative theoretical flange curling
Functional Analysis of Water Stress-Responsive Soybean GmNAC003 and GmNAC004 Transcription Factors in Lateral Root Development in Arabidopsis

In Arabidopsis, NAC (NAM, ATAF and CUC) transcription factors have been found to promote lateral root number through the auxin signaling pathway. In the present study, the role of water stress–inducible soybean GmNAC003 and GmNAC004 genes in the enhancement of lateral root development under water deficit conditions was investigated. Both genes were highly expressed in roots, leaves and flowers of soybean and were strongly induced by water stress and moderately induced by a treatment with abscisic acid (ABA). They showed a slight response to treatment with 2,4-dichlorophenoxyacetic acid (2,4-D). The transgenic Arabidopsis plants overexpressing GmNAC004 showed an increase in lateral root number and length under non-stress conditions and maintained higher lateral root number and length under mild water stress conditions compared to the wild-type (WT), while the transgenic plants overexpressing GmNAC003 did not show any response. However, LR development of GmNAC004 transgenic Arabidopsis plants was not enhanced in the water-stressed compared to the well-watered treatment. In the treatment with ABA, LR density of the GmNAC004 transgenic Arabidopsis was less suppressed than that of the WT, suggesting that GmNAC004 counteracts ABA-induced inhibition of lateral root development. In the treatment with 2,4-D, lateral root density was enhanced in both GmNAC004 transgenic Arabidopsis and WT plants but the promotion was higher in the transgenic plants. Conversely, in the treatment with naphthylphthalamic acid (NPA), lateral root density was inhibited and there was no difference in the phenotype of the GmNAC004 transgenic Arabidopsis and WT plants, indicating that auxin is required for the action of GmNAC004. Transcript analysis for a number of known auxin and ABA related genes showed that GmNAC004's role may suppress ABA signaling but promote auxin signaling to increase lateral root development in the Arabidopsis heterologous system.
Characterization of brain tumor initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors

CNS Primitive Neuroectodermal tumors (CNS-PNETs) are members of the embryonal family of malignant childhood brain tumors, which remain refractory to current therapeutic treatments. Current paradigm of brain tumorigenesis implicates brain tumor-initiating cells (BTIC) in the onset of tumorigenesis and tumor maintenance. However, despite their significance, there is currently no comprehensive characterization of CNS-PNETs BTICs. Recently, we described an animal model of CNS-PNET generated by orthotopic transplantation of human Radial Glial (RG) cells - the progenitor cells for adult neural stem cells (NSC) - into NOD-SCID mice brain and proposed that BTICs may play a role in the maintenance of these tumors. Here we report the characterization of BTIC lines derived from this CNS-PNET animal model. BTIC’s orthotopic transplantation generated highly aggressive tumors also characterized as CNS-PNETs. The BTICs have the hallmarks of NSCs as they demonstrate self-renewing capacity and have the ability to differentiate into astrocytes and early migrating neurons. Moreover, the cells demonstrate aberrant accumulation of wild type tumor-suppressor protein p53, indicating its functional inactivation, highly up-regulated levels of onco-protein cMYC and the BTIC marker OCT3/4, along with metabolic switch to glycolysis - suggesting that these changes occurred in the early stages of tumorigenesis. Furthermore, based on RNA- and DNA-seq data, the BTICs did not acquire any transcriptome-changing genomic alterations indicating that the onset of tumorigenesis may be epigenetically driven. The study of these BTIC self-renewing cells in our model may enable uncovering the molecular alterations that are responsible for the onset and maintenance of the malignant PNET phenotype.