Miracle-dz/UniFAR-FTUs huggingface dataset:
An Outbreak of Mycobacterium abscessus Infection in a Pediatric Intensive Care Unit in Kuwait

Background: Mycobacterium abscessus has been associated with respiratory tract infections, localized skin and soft tissue infections and sepsis. However, outbreaks of M. abscessus are rare. Aim: to report an outbreak of M. abscessus causing respiratory tract infections in a Pediatric Intensive Care Unit (PICU) in Kuwait, its investigation and control measures. Methods: Respiratory secretions were obtained from ventilator-dependent patients showing signs of sepsis, including fever, malaise and weight loss. The specimens were cultured on appropriate routine media. After the results of the sample taken from the index case as acid-fast bacilli positive, all patients were screened for M. abscessus carriage. Isolates were identified by INNO-LiPA Mycobacteria v2 line probe assay and DNA sequencing. Molecular fingerprinting DiversiLab strain typing was performed on the isolates. Epidemiologic investigation was conducted during the outbreak. Findings: the outbreak affected 5 patients, 4 of whom had severe infections including 1 patient with septicemia. Asymptomatic carriage of outbreak strain was found in 1 patient. All environmental samples were negative for M. abscessus but some were positive for M. gordonae and M. fortuitum. The source could not be identified. Stringent infection control measures were put in place, including reemphasizing hand hygiene and closure of the Pediatric Intensive Care Unit to new admissions. A year later, no further case has occurred after the last case. Conclusion: To our knowledge, this is the first report of a hospital-acquired outbreak of respiratory tract infection caused by M. abscessus in a Pediatric Intensive Care Unit. In the absence of definite source identification, reinforcement of standard infection control guidelines was successful in containing the outbreak.
Detecting Spatial Variations of Erythrocytes by Ultrasound Backscattering Statistical Parameters Under Pulsatile Flow

The echogenicity of whole blood is known to vary during the flow cycle under pulsatile flow both in vitro and in vivo. However, the fundamental underlying mechanisms remain uncertain. The combined effects of flow acceleration and the shear rate were recently used to explain the cyclic variations of signals backscattered from flowing blood. However, testing this hypothesis requires determination of the spatial distributions of red blood cells (RBCs) in flowing blood. Recently, the Nakagami (m) and scaling (Ω) parameters have been used, respectively, to detect the spatial distributions of RBCs and the intensity of backscattering signal from blood under steady flow. For a better understanding of the relationship between the spatial distributions of RBCs and erythrocyte aggregation under pulsatile flow condition, these ultrasound backscattering statistical parameters were used, in this study, to characterize signals backscattered from both whole blood and RBC suspensions at different peak flow velocities (from 10 to 30 cm/s) and hematocrits (20% and 40%). The experiments were carried out by a 35-MHz ultrasound transducer. The m and Ω parameters were calculated for different blood properties and conditions, and the flow velocity in the center of blood flowing through a tube was measured synchronously. In whole blood, the results demonstrated that most RBCs were aggregated progressively toward the center of tube as the flow velocity started to accelerate, and that the increase in the intensity of the backscattered signal envelope to a maximum was attributable to larger rouleaux being formed in the center of tube. This phenomenon became apparent at a lower peak flow velocity with 40% hematocrit. However, there were no cyclic and spatial variations of the backscattering signal over a pulsatile cycle in RBC suspensions.
ARP-1/COUP-TF II Determines Hepatoma Phenotype by Acting as Both a Transcriptional Repressor of Microsomal Triglyceride Transfer Protein and an Inducer of CYP7A1*

L35 and FAO cells were derived as single cell isolates from H35 cells. Whereas L35 cells do not express microsomal triglyceride transfer protein (MTP), which regulates lipoprotein secretion, they express CYP7A1, which regulates bile acid synthesis from cholesterol. FAO cells display the opposite phenotype (i.e. expression of MTP but not CYP7A1). We examined the molecular basis of the transcriptional inactivation of the MTP gene in L35 cells. Nested deletion and mutagenesis studies show that a conserved DR1 element within the 135-bp proximal MTP promoter is responsible for differential expression by L35 and FAO cells. Yeast one-hybrid screening identified apolipoprotein A1 regulatory protein-1/chicken ovalbumin upstream promoter transcription factor II (ARP-1/COUP-TFII) and retinoid X receptor (RXRα) as the protein factors that can bind to the conserved DR1 element. Nuclear extracts from L35 cells contained 2-fold more ARP-1/COUP-TFII and 50% less RXRα than those from FAO cells. Immunologic studies show that in L35 cells, ARP-1/COUP-TFII is bound to the DR1 element, whereas in FAO cells, a complex containing RXRα is bound to the DR1 element. Co-transfection studies show that ARP-1/COUP-TFII repressed MTP promoter activity by ∼70% in FAO hepatoma cells, whereas RXRα and its ligand 9-cis-retinoic acid increased MTP promoter activity by 6-fold in L35 cells. The combined data suggest that in the context of the MTP promoter, ARP-1/COUP-TFII (repressor) and a complex containing RXRα (inducer) compete for the DR1 element. Analysis of the CYP7A1 promoter revealed that it is ∼5-fold more active in L35 cells than in FAO cells. Co-transfection of an ARP-1/COUP-TFII expression vector showed that it enhances CYP7A1 promoter activity by 6-fold in FAO cells. These combined findings indicate that ARP-1/COUP-TFII acts as both a transcriptional repressor (of MTP) and as a transcription activator (of CYP7A1). This dual function of ARP-1/COUP-TFII may play an important role in determining the metabolic phenotype of individual liver cells.
The Caenorhabditis elegans UNC-87 protein is essential for maintenance, but not assembly, of bodywall muscle

Mutations in the unc-87 gene of Caenorhabditis elegans cause disorganization of the myofilament lattice in adult bodywall muscle. In order to assess the organization of specific bodywall muscle components in the absence of the unc-87 gene product, we examined the bodywall muscles of mutant animals using phalloidin and monoclonal antibodies to various muscle proteins. These studies indicated that the bodywall muscle of unc-87 embryos is initially almost wild type in its organization, but at later stages, the muscle becomes severely disorganized. To address the possibility that this disorganization is due to deterioration of the muscle as a result of contraction, we introduced into the unc-87 mutant background a mutation that decreases myosin heavy chain activity but does not substantially affect muscle structure. The improved muscle structure and motility of the double mutants are consistent with the hypothesis that at least part of the disorganization phenotype of unc-87 mutants is a consequence of the wild-type levels of force generated during muscle contraction. These results imply that the role of the unc-87 gene product is not in specifying organization but rather in serving as a structural component maintaining lattice integrity during and after contraction.
A NEW LOOK AT AN ANCIENT ORDER: GENERIC REVISION OF THE BANGIALES (RHODOPHYTA) 1

The red algal order Bangiales has been revised as a result of detailed regional studies and the development of expert local knowledge of Bangiales floras, followed by collaborative global analyses based on wide taxon sampling and molecular analyses. Combined analyses of the nuclear SSU rRNA gene and the plastid RUBISCO LSU (rbcL) gene for 157 Bangiales taxa have been conducted. Fifteen genera of Bangiales, seven filamentous and eight foliose, are recognized. This classification includes five newly described and two resurrected genera. This revision constitutes a major change in understanding relationships and evolution in this order. The genus Porphyra is now restricted to five described species and a number of undescribed species. Other foliose taxa previously placed in Porphyra are now recognized to belong to the genera Boreophyllum gen. nov., Clymene gen. nov., Fuscifolium gen. nov., Lysithea gen. nov., Miuraea gen. nov., Pyropia, and Wildemania. Four of the seven filamentous genera recognized in our analyses already have generic names (Bangia, Dione, Minerva, and Pseudobangia), and are all currently monotypic. The unnamed filamentous genera are clearly composed of multiple species, and few of these species have names. Further research is required: the genus to which the marine taxon Bangia fuscopurpurea belongs is not known, and there are also a large number of species previously described as Porphyra for which nuclear SSU ribosomal RNA (nrSSU) or rbcL sequence data should be obtained so that they can be assigned to the appropriate genus.
Emergence of Patterned Stem Cell Differentiation Within Multicellular Structures

The ability of stem cells to differentiate into specified lineages in the appropriate locations is vital to morphogenesis and adult tissue regeneration. Although soluble signals are important regulators of patterned differentiation, here we show that gradients of mechanical forces can also drive patterning of lineages. In the presence of soluble factors permitting osteogenic and adipogenic differentiation, human mesenchymal stem cells at the edge of multicellular islands differentiate into the osteogenic lineage, whereas those in the center became adipocytes. Interestingly, changing the shape of the multicellular sheet modulated the locations of osteogenic versus adipogenic differentiation. Measuring traction forces revealed gradients of stress that preceded and mirrored the patterns of differentiation, where regions of high stress resulted in osteogenesis, whereas stem cells in regions of low stress differentiated to adipocytes. Inhibiting cytoskeletal tension suppressed the relative degree of osteogenesis versus adipogenesis, and this spatial patterning of differentiation was also present in three‐dimensional multicellular clusters. These findings demonstrate a role for mechanical forces in linking multicellular organization to spatial differentials of cell differentiation, and they represent an important guiding principle in tissue patterning that could be exploited in stem cell‐based therapies.
Acquisition and Persistence of Human Papillomavirus Infection in Younger Men: A Prospective Follow-up Study among Danish Soldiers

No data is yet available on incidence or persistence of human papillomavirus (HPV) infection in men. We enrolled 374 younger male conscripts (18-29 years) in a prospective study, and they were examined twice with an interval of 6 to 8 months. Data collection included a questionnaire and a sample of cells from the penis for HPV detection using PCR. In addition, the presence of Chlamydia trachomatis DNA was assessed in urine samples by means of PCR. The HPV prevalence at the first and second examinations was 33.8% and 31.9%, respectively. The acquisition rate of HPV (overall) during follow-up was 13.8%, and nearly one fourth of the participants were HPV positive at both examinations. Number of sex partners during follow-up was the most important risk factor for acquiring HPV (odds ratio, 17.2; 95% confidence interval, 4.6-64.7, for ≥3 partners versus ≤1 partner). In contrast, acquisition of a new HPV type in initially HPV-positive men was strongly related to having multiple HPV types at enrollment (OR, 4.1; 95% confidence interval, 1.4-12.3). This was also the most important risk factor for HPV persistence together with current smoking and having a high-risk HPV type at enrollment. This is the first study to assess risk factors for acquisition and persistence of HPV. The sexually transmitted nature of the infection is confirmed, and the data point to an important role of having multiple HPV types for persistence.
Neural Processing of Repetition and Non-Repetition Grammars in 7- and 9-Month-Old Infants

An essential aspect of infant language development involves the extraction of meaningful information from a continuous stream of auditory input. Studies have identified early abilities to differentiate auditory input along various dimensions, including the presence or absence of structural regularities. In newborn infants, frontal and temporal regions were found to respond differentially to these regularities (Gervain et al., 2008), and in order to examine the development of this abstract rule learning we presented 7- and 9-month-old infants with syllables containing an ABB pattern (e.g., “balolo”) or an ABC pattern (e.g., “baloti”) and measured activity in left and right lateral brain regions using near-infrared spectroscopy (NIRS). While prior newborn work found increases in oxyhemoglobin (oxyHb) activity in response to ABB blocks as compared to ABC blocks in anterior regions, 7- and 9-month-olds showed no differentiation between grammars in oxyHb. However, changes in deoxyhemoglobin (deoxyHb) pointed to a developmental shift, whereby 7-month-olds showed deoxyHb responding significantly different from zero for ABB blocks, but not ABC blocks, and 9-month-olds showed the opposite pattern, with deoxyHb responding significantly different from zero for the ABC blocks but not the ABB blocks. DeoxyHb responses were more pronounced over anterior regions. A grammar by time interaction also illustrated that during the early blocks, deoxyHb was significantly greater to ABC than in later blocks, but there was no change in ABB activation over time. The shift from stronger activation to ABB in newborns (Gervain et al., 2008) and 7-month-olds in the present study to stronger activation to ABC by 9-month-olds here is discussed in terms of changes in stimulus salience and novelty preference over the first year of life. The present discussion also highlights the importance of future work exploring the coupling between oxyHb and deoxyHb activation in infant NIRS studies.
Neurofibromatosis type 1 and sporadic optic gliomas

Aims: To compare the natural history of sporadic optic glioma with those associated with neurofibromatosis type 1 (NF1). Methods: Optic glioma cases were identified using both the Manchester Children's Tumour Registry (CTR) and the North West Regional NF1 Database (NF1DB), with detailed information on natural history available from the former (in 34 of 36 cases identified). Results: A total of 52 cases over a period of 41 years were identified. From the 34 whose natural history was known, almost all (n = 31) were symptomatic, with mean ages of presentation of 4.5 and 5.1 years for NF1 and sporadic cases respectively. The majority (n = 22) presented with visual impairment, seven of whom were blind in at least one eye. Sporadic cases were over twice as likely as NF1 to have visual impairment. Recurrence occurred in 12 patients. Fewer NF1 patients died as a direct result of their optic glioma, but overall mortality and 5 and 10 year survival rates between the two groups were similar. All five primary (non-metastatic) second central nervous system (CNS) tumours occurred in NF1 cases, two of these following radiotherapy. Conclusions: Symptomatic sporadic optic gliomas presented with impaired vision more frequently and were more aggressive than NF1 optic gliomas. Only optic glioma cases with NF1 were at risk of developing a second CNS tumour. Aggressive treatment of sporadic optic gliomas and early surveillance of NF1 optic gliomas may be required. The use of radiotherapy in these children requires further clarification.
Legacy Effects in Radical Innovation: A Study of European Internet Banking

How do firms cope with the challenges of disruptive change in their industry? Numerous studies have highlighted that success with any prior technology creates a negative legacy effect for the next radical technological shift. We question the overly pessimistic view of such legacy effects and ask how quickly firms embrace technological breakthroughs by radically innovating and who wins in the longer term? In this paper, we argue that legacy is a multi-faceted construct whose diverse aspects could simultaneously have different effects on innovation speed and market performance. We identify three main types of legacy related to technology, organizational, and country-level influences. Previous research tends to focus on technological or market effects in isolation, whereas we seek to study the effects of both firm and country legacy simultaneously on speed to radical innovation and market performance over time. Based on a conceptual framework we develop six hypotheses concerning the legacy effects on initial speed radical innovation and subsequent market performance. We chose the European retail banking industry and the focal innovation of transactional Internet banking as a suitable empirical context to employ quantitative hypothesis testing. Detailed and longitudinal (1996-2001) data were collected for a sample of 123 banks from six European countries: United Kingdom, Germany, France, Sweden, Finland, and Denmark. We specified a model and used threestage least squares (3SLS) as a method to estimate simultaneous regression equations due to endogeneity of a key variable. We show that the prevailing negative view of legacies is likely to be overstated.
Pose Analysis of Alpha-Carbons in Proteins

In this paper we present a novel method to describe the pose (position and orientation) distribution of amino acid residue pairs within a protein, which are proximal in space and distal in sequence. While the Ramachandran plot provides information of protein conformations using the φ and ψ angles between sequentially proximal residues, our method can offer six-dimensional relative pose information. Distribution data are visualized in the form of continuous distributions by using Gaussian distribution functions on SO(3) and R3. Hence, we discuss how the classical Gaussian functions can be generalized to capture both positional and orientational data. The method is applied to 168 protein structures in the Protein Data Bank and results are discussed.
Overexpression of HuR, a nuclear–cytoplasmic shuttling protein, increases the in vivo stability of ARE‐containing mRNAs

The messenger RNAs of many proto‐oncogenes, cytokines and lymphokines are targeted for rapid degradation through AU‐rich elements (AREs) located in their 3′ untranslated regions (UTRs). HuR, a ubiquitously expressed member of the Elav family of RNA binding proteins, exhibits specific affinities for ARE‐containing RNA sequences in vitro which correlate with their in vivo decay rates, thereby implicating HuR in the ARE‐mediated degradation pathway. We have transiently transfected HuR into mouse L929 cells and observed that overexpression of HuR enhances the stability of β‐globin reporter mRNAs containing either class I or class II AREs. The increase in mRNA stability parallels the level of HuR overexpression, establishing an in vivo role for HuR in mRNA decay. Furthermore, overexpression of HuR deletion mutants lacking RNA recognition motif 3 (RRM 3) does not exert a stabilizing effect, indicating that RRM 3 is important for HuR function. We have also developed polyclonal anti‐HuR antibodies. Immunofluorescent staining of HeLa and L929 cells using affinity‐purified anti‐HuR antibody shows that both endogenous and overexpressed HuR proteins are localized in the nucleus. By forming HeLa–L929 cell heterokaryons, we demonstrate that HuR shuttles between the nucleus and cytoplasm. Thus, HuR may initially bind to ARE‐containing mRNAs in the nucleus and provide protection during and after their export to the cytoplasmic compartment.
Automatic Counting Cancer Cell Colonies using GIEA for TSK-type Neural Fuzzy Network

This paper proposes a TSK-type neural fuzzy network (TNFN) with a group interaction-based evolutionary algorithm (GIEA) for constructing the cancer cell colonies diagnosis system (CCCDS). The proposed GIEA is designed on the basis of symbiotic evolution which each chromosome in the population represents only partial solution. The whole solution consists of several chromosomes. The GIEA is different from the traditional symbiotic evolution. Each population in the GIEA is divided into several groups. Each group represents a set of the chromosomes that belongs to only one fuzzy rule. Moreover, in the GIEA, the interaction ability is considered that the chromosomes will interact with other groups to generate the better chromosomes by elites-base interaction crossover strategy (EICS). In the CCCDS, the EICS is used to train the CCCDS. After trained by the EICS, the CCCDS can diagnose the visible cancer cell colonies automatically. The performance of the GIEA is proved to be better than other existing models in diagnosing cancer cell colonies.
Autogenous Laser Keyhole Welding of AISI 316LTi

Effective autogenous full-penetration welding of 4 mm thick AISI 316LTi austenitic stainless steel bars was achieved using a CO2 laser. The welding process parameters required to obtain an optimal and repeatable procedure giving the best quality welds were identified. The use of side jet of gas suppressing plasma formation was investigated, and it was discovered that there are optimal conditions that result in increased power transmission and improved repeatability. Tests were carried out on the final welds in the as-welded state and in the annealed state. These included microstructural and X-ray diffraction (XRD) analysis as well as potentiodynamic and salt spray corrosion tests. Microstructural analysis showed that solidification occurred in primary ferrite solidification (FA) mode. Application of a heat treatment to the welded samples dissolved the ferrite, but resulted in carbide precipitation diminishing resistance to pitting, and the corrosion tests carried out demonstrated that the corrosion-resistant properties of the material were not compromised by the welding process, and that a post-process heat treatment was unnecessary.
Irinotecan-Induced Gastrointestinal Dysfunction and Pain Are Mediated by Common TLR4-Dependent Mechanisms

Strong epidemiological data indicate that chemotherapy-induced gut toxicity and pain occur in parallel, indicating common underlying mechanisms. We have recently outlined evidence suggesting that TLR4 signaling may contribute to both side effects. We therefore aimed to determine if genetic deletion of TLR4 improves chemotherapy-induced gut toxicity and pain. Forty-two female wild-type (WT) and 42 Tlr4 null (−/−) BALB/c mice weighing between 18 and 25 g (10–13 weeks) received a single 270 mg/kg (i.p.) dose of irinotecan hydrochloride or vehicle control and were killed at 6, 24, 48, 72, and 96 hours. Bacterial sequencing was conducted on cecal samples of control animals to determine the gut microbiome profile. Gut toxicity was assessed using validated clinical and histopathologic markers, permeability assays, and inflammatory markers. Chemotherapy-induced pain was assessed using the validated rodent facial grimace criteria, as well as immunologic markers of glial activation in the lumbar spinal cord. TLR4 deletion attenuated irinotecan-induced gut toxicity, with improvements in weight loss (P = 0.0003) and diarrhea (P < 0.0001). Crypt apoptosis was significantly decreased in BALB/c-Tlr4−/−billy mice (P < 0.0001), correlating with lower mucosal injury scores (P < 0.005). Intestinal permeability to FITC-dextran (4 kDa) and LPS translocation was greater in WT mice than in BALB/c-Tlr4−/−billy (P = 0.01 and P < 0.0001, respectively). GFAP staining in the lumbar spinal cord, indicative of astrocytic activation, was increased at 6 and 72 hours in WT mice compared with BALB/c-Tlr4−/−billy mice (P = 0.008, P = 0.01). These data indicate that TLR4 is uniquely positioned to mediate irinotecan-induced gut toxicity and pain, highlighting the possibility of a targetable gut/CNS axis for improved toxicity outcomes. Mol Cancer Ther; 15(6); 1376–86. ©2016 AACR.