Miracle-dz/UniFAR-FTUs huggingface dataset:
Community Structure and Activity of a Highly Dynamic and Nutrient-Limited Hypersaline Microbial Mat in Um Alhool Sabkha, Qatar

The Um Alhool area in Qatar is a dynamic evaporative ecosystem that receives seawater from below as it is surrounded by sand dunes. We investigated the chemical composition, the microbial activity and biodiversity of the four main layers (L1–L4) in the photosynthetic mats. Chlorophyll a (Chl a) concentration and distribution (measured by HPLC and hyperspectral imaging, respectively), the phycocyanin distribution (scanned with hyperspectral imaging), oxygenic photosynthesis (determined by microsensor), and the abundance of photosynthetic microorganisms (from 16S and 18S rRNA sequencing) decreased with depth in the euphotic layer (L1). Incident irradiance exponentially attenuated in the same zone reaching 1% at 1.7-mm depth. Proteobacteria dominated all layers of the mat (24%–42% of the identified bacteria). Anoxygenic photosynthetic bacteria (dominated by Chloroflexus) were most abundant in the third red layer of the mat (L3), evidenced by the spectral signature of Bacteriochlorophyll as well as by sequencing. The deep, black layer (L4) was dominated by sulfate reducing bacteria belonging to the Deltaproteobacteria, which were responsible for high sulfate reduction rates (measured using 35S tracer). Members of Halobacteria were the dominant Archaea in all layers of the mat (92%–97%), whereas Nematodes were the main Eukaryotes (up to 87%). Primary productivity rates of Um Alhool mat were similar to those of other hypersaline microbial mats. However, sulfate reduction rates were relatively low, indicating that oxygenic respiration contributes more to organic material degradation than sulfate reduction, because of bioturbation. Although Um Alhool hypersaline mat is a nutrient-limited ecosystem, it is interestingly dynamic and phylogenetically highly diverse. All its components work in a highly efficient and synchronized way to compensate for the lack of nutrient supply provided during regular inundation periods.
A systematic study of hcp crystal orientation and morphology effects in polycrystal deformation and fatigue

Elastically anisotropic, physically based, length-scale- and rate-dependent crystal plasticity finite element investigations of a model hcp polycrystal are presented and a systematic study was carried out on the effects of combinations of crystallographic orientations on local, grain-level stresses and accumulated slip in cycles containing cold dwell. It is shown that the most damaging combination is the one comprising a primary hard grain with c-axis near-parallel to the loading direction and an adjacent soft grain having c-axis near-normal to the load and a prismatic slip plane at approximately 70° to the normal to the load. We term such a combination a rogue grain combination. In passing, we compare results with the Stroh model and show that even under conditions of plasticity in the hcp polycrystal, the Stroh model qualitatively predicts some of the observed behaviours. It is shown that under very particular circumstances, a morphological–crystallographic interaction occurs which leads to particularly localized accumulated slip in the soft grain and the penetration of the slip into the adjacent hard grain. The interaction effect occurs only when the (morphological) orientation of the grain boundary in the rogue grain combination coincides (within approximately ±5°) with the (crystallographic) orientation of an active slip system in the soft grain. It is argued that the rogue grain combination and the morphological–crystallographic interaction are responsible for fatigue facet formation in Ti alloys with cold dwell, and a possible mechanism for facet formation is presented. The experimental observations of fatigue facet formation have been reviewed and they provide considerable support for the conclusions from the crystal plasticity modelling. In particular, faceting was found to occur at precisely those locations predicted by the model, i.e. at a rogue grain combination. Some experimental evidence for the need for a crystallographic–morphological interaction in faceting is also presented.
Crowdsourcing the creation of image segmentation algorithms for connectomics

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This “deep learning” approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from cooperation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test dataset. Retrospective evaluation of the challenge scoring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge.
Detection of Network Faults and Performance Problems

Network normal operation baselining for automatic detection of anomalies is addressed. A model for network traffic is presented in which studied variables are modeled as a finite mixture model. Based on stochastic approximation of the maximum likelihood function, we propose a baseline of network normal operation as the asymptotic distribution of the difference between successive estimates of model parameters. The baseline multivariate random variable is shown to be stationary, with mean zero under normal operation. Performance problems are characterized by sudden jumps in the mean. Detection is formulated as an online change point problem, where the task is to process residuals and raise alarms as soon as anomalies occur. An analytical expression of false alarm rate allows us to choose the threshold, automatically. Extensive experimental results on a real network showed that the monitoring agent is able to detect even slight changes in the characteristics of the network, and adapt to traffic patterns, while maintaining a low alarm rate. Despite large fluctuations in network traffic, this work proves that tailoring traffic modeling to specific goals can be efficiently achieved.
The transmission mechanism of monetary policy: Analysing the financial market pass-through

This paper uses a structural vector autoregressive approach to identify the e? ects of monetary policy innovations on di? erent sub-markets of the Icelandic financial system. This forms the first stage of the interest rate channel of the monetary transmission mechanism, with the second stage explaining the propagation of monetary policy from the financial markets to the real economy. The results indicate that an innovation to monetary policy has a significant within-the-month e? ect on the money market rate. The innovation is then propagated through the money market to the bond market and from there to the bank loan rate market, with the e? ect peaking one to four months after the initial monetary policy shock and lasting for about eight to nine months. The results suggest that the bond rate is the most important determinant of the marginal cost of loan funding. This could be explained by mark-up pricing of loans over deposits with some type of adjustment costs explaining the sluggish response of the bank loan rate to shocks in the marginal cost of loan funding.
Marked Intratumoral Heterogeneity of c-myc and CyclinD1 But Not of c-erbB2 Amplification in Breast Cancer

Intratumoral heterogeneity mirrors subclonal diversity and might affect treatment response. To investigate molecular heterogeneity of primary breast cancer specimens, we determined the amplification status of growth regulatory genes (c-erbB2, topoisomerase IIα, c-myc, and cyclinD1) in macroscopically and microscopically separate areas of individual tumors (n = 21). Using laser-assisted microdissection and quantitative PCR, we found marked intratumoral heterogeneity with different patterns for each gene. Molecular heterogeneity in amplification pattern could be demonstrated between both macroscopically (0.5 to several centimeters) and microscopically (10 to several hundred micrometers) distant tumor areas. C-erbB2 amplification proved to be the most stable amplification in individual tumors, with heterogeneity occurring in only 36% of amplified cases. By contrast, amplification of c-myc and cyclinD1 revealed varying patterns in the vast majority of amplified cases (100% and 83%). The constancy of c-erbB2 amplification underlines its presumed importance in breast cancer biology. We conclude that the molecular heterogeneity of breast cancer as evidenced in this study requires thorough and representative sampling of different tumor areas when the biologic significance of somatic mutations is considered. Patterns of heterogeneity can be used to trace the clonal evolution within different compartments of an individual tumor.
Face Recognition Using 2-D, 3-D, and Infrared: Is Multimodal Better Than Multisample?

This work examines face recognition using normal intensity images, infrared images, three-dimensional shape, and combinations of these. We compare the performance improvement obtained by combining three-dimensional or infrared with normal intensity images (a "multimodal" approach) to the performance improvement obtained by using multiple intensity images (a "multisample" approach). Combining results from different types of imagery gives significantly higher recognition rates than are obtained by using a single intensity image. However, significantly higher recognition rates are also obtained by combining results from multiple intensity images. Overall, initial results indicate that, using an "eigen-face" recognition algorithm and weighted score fusion, multisample techniques can result in a performance increase comparable to that of multimodal techniques
Adequacy of food spending is related to housing expenditures among lower-income Canadian households

Abstract Objectives A number of studies have pointed to the pressure that housing costs can exert on the resources available for food. The objectives of the present study were to characterise the relationship between the proportion of income absorbed by housing and the adequacy of household food expenditures across the Canadian population and within income quintiles; and to elucidate the impact of receipt of a housing subsidy on adequacy of food expenditures among low-income tenant households. Design The 2001 Survey of Household Spending, conducted by Statistics Canada, was a national cross-sectional survey that collected detailed information on expenditures on goods and services. The adequacy of food spending was assessed in relation to the cost of a basic nutritious diet. Setting Canada. Subjects The person with primary responsibility for financial maintenance from 15 535 households from all provinces and territories. Results As the proportion of income allocated to housing increased, food spending adequacy declined significantly among households in the three lowest income quintiles. After accounting for household income and composition, receipt of a housing subsidy was associated with an improvement in adequacy of food spending among low-income tenant households, but still mean food spending fell below the cost of a basic nutritious diet even among subsidised households. Conclusions This study indicates that housing costs compromise the food access of some low-income households and speaks to the need to re-examine policies related to housing affordability and income adequacy.
Non-perturbative F-terms across lines of BPS stability

We consider non-perturbative terms in the 4d effective action due to BPS D-brane instantons, and study their continuity properties in moduli space as instantons cross lines of BPS stability, potentially becoming non-BPS. We argue that BPS instantons contributing to the superpotential cannot become non-BPS anywhere in moduli space, since they cannot account for the required four goldstino fermion zero modes. At most they can reach lines of threshold stability, where they split into mutually BPS multi-instantons, as already discussed in the literature. On the other hand, instantons with additional fermion zero modes, contributing to multi-fermion F-terms, can indeed cross genuine lines of marginal stability, beyond which they lead to non-BPS systems. The non-BPS instanton generates an operator which is a D-term locally in moduli space, but not globally. This is due to a cohomological obstruction localized on the BPS locus, where the D-term must be written as an F-term, thus ensuring the continuity of the 4d contribution to the effective action. We also point out an interesting relation between lifting of fermion zero modes on instantons and 4d supersymmetry breaking.
Clinical presentation and outcome of autosomal dominant polycystic kidney disease in Pakistan: a single center experience.

OBJECTIVE To delineate clinical presentation and outcome of Autosomal Dominant Polycystic Kidney Disease (ADPKD) in terms of need for renal replacement therapy of kidney transplantation in Pakistani patients. METHODS Patients with ADPKD were identified using strict clinical criteria. Medical charts were evaluated retrospectively for initial presenting complaints, co-morbids, family history of ADPKD, any palpable mass on abdominal examination, cardiac examination for any abnormal finding and use of any anti-hypertensive drugs. Laboratory parameters were assessed. Chi square and Logistic regression analyses at 95% CI were used for statistical significance. A p value of less 0.05 was considered statistically significant. RESULTS A total of 56 patients fulfilled our criteria of ADPKD. There were 40 (71.4%) males and 16 (28.6%) females in our study. The mean age at the time of diagnosis of ADPKD was 47.0 +/- 14.5 years. Mean follow up period for all patients was 7.6 +/- 4.2 years. Most common form of presentation was hypertension in 38 (67.9%) patients. Kidneys were palpable in 33 (58.9%), liver in 16 (28.6%) and spleen in 6 patients (10.7%). Microscopic haematuria was observed in 38 (67.8%) patients while gross haematuria was present in 10 (17.9%) patients. The murmur of mitral valve prolapse was found in 10 patients on clinical examination which was later confirmed on transthoracic echocardiography (TEE). On MRI/MRA 2 (3.6%) patients each had berry aneurysm and AV malformations. Three patients (5.4%) received renal transplant and 19 (33.9%) patients were dialysis dependent at the end of study. A total 11 (20%) were lost to follow up. Two patients (3.5%) died during six years follow up. Male sex and uncontrolled hypertension were most important predictors of poor prognosis (p < 0.03 and < 0.048 respectively). CONCLUSION Pre-symptomatic patients with ADPKD should be monitored with blood pressure measurements and assessment of their renal function. The advantages of such monitoring include the ability to prevent or control infection and hypertension, to identify potential kidney donors from among the family, to offer advice on marriage and childbearing, and to provide prenatal diagnosis.
Adherence to treatment of chronic hepatitis C: from interferon containing regimens to interferon and ribavirin free regimens

Abstract Patients’ experience during treatment may affect treatment adherence. Our aim was to assess the impact of patient-reported outcomes (PROs) on adherence to different anti-hepatitis C virus (HCV) regimens. Clinical, demographic, and PRO data (short form-36 [SF-36], chronic liver disease questionnaire-hepatitis C version [CLDQ-HCV], functional assessment of chronic illness therapy-fatigue [FACIT-F], work productivity and activity impairment: specific health problem [WPAI:SHP]) from 13 multinational clinical trials of anti-HCV treatment were available. Treatment adherence was defined as >80% of prescribed doses taken. Included were 4825 HCV patients. Regimens were grouped into: interferon- and ribavirin (RBV)-containing (±sofosbuvir [SOF]), interferon-free RBV-containing (RBV + SOF ± ledipasvir [LDV]), and interferon-free RBV-free (LDV/SOF). The adherence to these regimens were 77.6%, 84.3%, and 96.2%, respectively (P < 0.0001). Nonadherent patients were more likely to be unemployed and to have a greater PRO impairment at baseline (up to −5.3% lower PRO scores, P < 0.0001). During treatment with interferon- or RBV-based regimens, nonadherent patients experienced lower PROs and had larger decrements from their baseline PRO scores. In contrast, there were no significant declines in PRO scores (all P > 0.05) for the small number of patients who were nonadherent to LDV/SOF. In multivariate analysis, being treatment-naive, longer treatment duration, and receiving an interferon- or RBV-containing regimen were associated with a lower likelihood of adherence (all P < 0.003). Better baseline and on-treatment PRO scores were associated with a higher likelihood of adherence to interferon and RBV. The use of interferon and/or RBV, longer duration of treatment, and lower baseline and on-treatment PRO scores were linked to a decreased likelihood of being adherent to interferon + RBV-containing or interferon-free RBV-containing antiviral regimens. Interferon- and RBV-free regimens were associated with excellent adherence.
Are the Symptoms of Calcific Tendinitis Due to Neoinnervation and/or Neovascularization?

BACKGROUND Calcific tendinitis can be a substantial cause of pain and dysfunction in the shoulder, and the pathophysiology is unclear. Recent studies have shown a link among nerve ingrowth, neovascularization, and pain in tendinopathy. The aim of this study was to determine whether there is evidence of neoinnervation and/or neovascularization in calcific tendinitis lesions of the shoulder. METHODS At arthroscopy, ultrasound was used to identify calcium within the tendon. Samples were taken from the supraspinatus tendon adjacent to the calcific lesion (in the calcific tendinitis group, with ten patients), the torn supraspinatus tendon of patients undergoing rotator cuff repair (the rotator cuff tear group, with ten patients), and the subscapularis tendon of patients undergoing a stabilization surgical procedure (the control group, with ten patients). Biopsied tendon samples were evaluated immunohistochemically by quantifying the presence of macrophages (using CD68 and CD206), T cells (CD3), mast cells (mast cell tryptase), vascular endothelium (CD34), and peripheral nerve markers (PGP 9.5). RESULTS There was a twofold to eightfold increase of nerve markers, neovascularization, macrophages, M2 macrophages, and mast cells in the calcific tendinitis group compared with the rotator cuff tear group (p < 0.001) and the control group (p < 0.001). Increased nerve counts positively correlated with more frequent extreme pain (r = 0.5, p < 0.01) and with increased neovascularization (r = 0.7, p < 0.01) and counts of CD68 macrophages (r = 0.8, p < 0.01), M2 macrophages (r = 0.6, p < 0.01), and mast cells (r = 0.7, p < 0.01). CONCLUSIONS This is the first study to show a significant increase in neovascularization and neoinnervation in calcific tendinitis lesions of the shoulder along with an eightfold increase in mast cells and macrophages. The findings are consistent with the hypothesis that, in calcific tendinitis, the calcific material is inducing a vigorous inflammatory response within the tendon with formation of new blood vessels and nerves. CLINICAL RELEVANCE This study helps to explain why calcific tendinitis is related to substantial pain in the clinical setting.
Increased acetylation of microtubules rescues human tau-induced microtubule defects and neuromuscular junction abnormalities in Drosophila

ABSTRACT Tau normally associates with and stabilizes microtubules (MTs), but is hyperphosphorylated and aggregated into neurofibrillary tangles in Alzheimer's disease and related neurodegenerative diseases, which are collectively known as tauopathies. MTs are regulated by different forms of post-translational modification, including acetylation; acetylated MTs represent a more stable microtubule population. In our previous study, we showed that inhibition of histone deacetylase 6 (HDAC6), which deacetylates tubulin at lysine 40, rescues defects in MTs and in neuromuscular junction growth caused by tau overexpression. However, HDAC6 also acts on other proteins that are involved in distinct biological processes unrelated to tubulins. In order to examine directly the role of increased tubulin acetylation against tau toxicity, we generated a site-directed α-tubulinK40Q mutation by CRISPR/Cas9 technology to mimic the acetylated MTs and found that acetylation-mimicking α-tubulin rescued tau-induced MT defects and neuromuscular junction developmental abnormalities. We also showed that late administration of ACY-1215 and tubastatin A, two potent and selective inhibitors of HDAC6, rescued the tau-induced MT defects after the abnormalities had already become apparent. Overall, our results indicate that increasing MT acetylation by either genetic manipulations or drugs might be used as potential strategies for intervention in tauopathies. Highlighted Article: Increased acetylation of microtubules by genetic and pharmacological approaches rescues human tau overexpression-induced toxicity in Drosophila muscles and neurons.
The role of low-molecular-weight oxidized materials in the adhesion properties of corona-treated polypropylene film

The effects of low-molecular-weight oxidized materials generated by corona treatment on the adhesion properties of polypropylene (PP) film were investigated by adhering four different materials to the modified PP: a polyamide printing ink, vapor-coated aluminum, a synthetic-rubber pressure-sensitive adhesive, and an acrylate-based pressure-sensitive adhesive. The low-molecularweight materials enhanced the adhesion of the ink and acrylate-based material, but hindered the adhesion of the metal and the rubber-based adhesive. This seemingly contradictory adhesion behavior can be readily explained using the principles outlined by Brewis and Briggs in the 1980s.
Silicon (Si) containing bone cements: a review

The purpose of this paper is to review the current status of silicon (Si)-containing bone cements. It is known that such cements have been in use for a while because of the tremendous societal needs and the unique role that Si plays in enhancing the effectiveness of the cements. The related discussion covers the composition, hardening mechanism, performances of cements of inorganic phases and inorganic-organic phases. This paper attempts to give a broad overview of Si-containing bone cements with significant features. The progress in the field is addressed while providing thoughts for future development of Si-containing bone cements.