Miracle-dz/UniFAR-FTUs huggingface dataset:
Light-Stimulated Bacterial Production and Amino Acid Assimilation by Cyanobacteria and Other Microbes in the North Atlantic Ocean

ABSTRACT We examined the contribution of photoheterotrophic microbes—those capable of light-mediated assimilation of organic compounds—to bacterial production and amino acid assimilation along a transect from Florida to Iceland from 28 May to 9 July 2005. Bacterial production (leucine incorporation at a 20 nM final concentration) was on average 30% higher in light than in dark-incubated samples, but the effect varied greatly (3% to 60%). To further characterize this light effect, we examined the abundance of potential photoheterotrophs and measured their contribution to bacterial production and amino acid assimilation (0.5 nM addition) using flow cytometry. Prochlorococcus and Synechococcus were abundant in surface waters where light-dependent leucine incorporation was observed, whereas aerobic anoxygenic phototrophic bacteria were abundant but did not correlate with the light effect. The per-cell assimilation rates of Prochlorococcus and Synechococcus were comparable to or higher than those of other prokaryotes, especially in the light. Picoeukaryotes also took up leucine (20 nM) and other amino acids (0.5 nM), but rates normalized to biovolume were much lower than those of prokaryotes. Prochlorococcus was responsible for 80% of light-stimulated bacterial production and amino acid assimilation in surface waters south of the Azores, while Synechococcus accounted for on average 12% of total assimilation. However, nearly 40% of the light-stimulated leucine assimilation was not accounted for by these groups, suggesting that assimilation by other microbes is also affected by light. Our results clarify the contribution of cyanobacteria to photoheterotrophy and highlight the potential role of other photoheterotrophs in biomass production and dissolved-organic-matter assimilation.
Isolation of Six Microorganisms from Rotten Dioscorea alata (Water Yam), and Antimicrobial Sensitivity Test with Nine Plant Extracts

Six microorganisms: four fungi—Aspergillus niger, Aspergillus flavus, Rhizopus stolonifera, Penicillium marneffei, two bacteria—Erwinia carotovora and Pseudomonas aeruginosa were isolated and identified from three rotten Dioscorea alata (water yam) varieties from two sites each in two local government areas of Benue State, Nigeria, in West Africa, between the months of May 2014 and May 2015. Pathogenicity test carried out using the microorganisms confirmed them to be the pathological agents of the rot. Antimicrobial activity test with aqueous extracts of nine plants: Terminalia catapa, Passiflora edulis, Daniella oliveri, Ceiba pentandra, Jatropha tanjorensis, Azadirachta indica, Carica papaya, Moringa oleifera, and Mangifera indica of fresh and dry material showed that three pathogens, Rhizopus stolonifera (fungi), Erwinia carotovora and Pseudomonas aeruginosa (bacteria) isolated were completely inhibited each by a plant. The result obtained shows that Passiflora edulis had the best antimicrobial activity for both fungi and bacteria; indeed it inhibited completely Rhizopus stolonifera which was stubborn with most of the other plants. Azadirachta indica, Carica papaya, Moringa oleifera, and Mangifera indica were also able to inhibit most of the fungi but not completely. Terminalia catapa and Jatropha tanjorensis were most effective against the bacteria. Erwinia carotovora was completely inhibited by Terminalia catapa and Pseudomonas aeruginosa was completely inhibited by Jatropha tanjorensis. Daniella oliveri and Ceiba pentandra had the least inhibition against the isolates. Generally, the fresh plant extract shows more activity as compared to the dry plant extract.
The health–promoting workplace: an integrative perspective

Abstract: The workplace is an important setting, affecting the physical, mental, economic and social wellbeing of workers, and, in turn, their families. Health of workers has many determinants, and a multidisciplinary, integrated approach is important. An overview of trends in workplace health promotion shows that current thinking has changed from a narrowly based risk–factors approach aimed at individual behaviour changes, to an integrative approach aimed at creating health–promoting workplaces. The health–promoting workplace has ‘an all—encompassing approach that empowers workers and employers to improve all facets of their health’. There are gaps in knowledge, at the state and national levels, relevant to the planning and assessment of workplace health. A national information network is needed to facilitate better links between public health practitioners and researchers in advancing the health of working Australians.
Non-cirrhotic portal fibrosis at a tertiary care centre in South India

Background Non-cirrhotic portal fibrosis (NCPF) is one of the important causes of upper gastrointestinal haemorrhage in patients in tropical countries. The aim of this study was to describe the clinical and laboratory profile of 68 patients with NCPF. Material and Methods NCPF is defined as liver disease with: (1) evidence of portal hypertension; (2) a liver biopsy showing no cirrhosis or a Tc-labelled sulphur colloid scan showing a pattern suggestive of NCPF; and (3) a patent splenoportal axis. The clinical, laboratory and demographic features of 68 patients with such criteria were studied and analysed. Results NCPF was common in women (73.5%) in the fourth decade of life. The median duration of illness was 24 months (range, 1 month–28 years). Patients presented to hospital with the sensation of a mass in the abdomen (50%) or with haematemesis (26.5%). They had splenomegaly (95.6%) and thrombocytopenia (88.2%). The majority of patients had normal liver function tests. Abdominal ultrasonography showed increased periportal and peri gallbladder echoes (72%), spontaneous collaterals (41.2%) and ascites (19.1%). Liver biopsy revealed portal venous sclerosis (76.3%) and periportal fibrosis (55.3%). Tc-labelled sulphur colloid scan was suggestive of NCPF in the remaining 30 cases. Conclusion NCPF is common in South India. Transient ascites occurs due to decompensation of liver function after variceal bleeding and in long standing cases of NCPF. Our study used Tc-sulphur scan for diagnosing NCPF in patients where liver biopsy was contraindicated in view of severe thrombocytopenia; however, the diagnostic utility of Tc-sulphur nuclear scan to diagnose NCPF in patients with severe hypersplenism needs to be further evaluated in future studies.
Characterization of a Ca2+‐ATPase in osteoclast plasma membrane

The plasma membrane fraction of chicken osteoclasts was purified utilizing 20% continuous Percoll gradients. Biochemical marker enzyme analysis (ouabain‐sensitive Na+, K+‐ATPase and 5′‐nucleotidase) indicated that plasma membrane enrichment was 11.87‐fold and 7.25‐fold, respectively, and contamination with mitochondria, endoplasmic reticulum, and lysosomes was low as determined by succinic dehydrogenase, NADH dehydrogenase, and N‐acetylglucosaminidase activities, respectively. SDS latency of Na+K+‐ATPase and 5′‐nucleotidase activities of the isolated plasma membranes revealed that 43‐50% of vesicles were sealed, with 10‐16% in the inside‐out orientation, depending on the membrane fraction used. Electron microscopy confirmed the vesicular nature of the plasma membrane fraction. The plasma membrane Ca2+‐ATPase had a high‐affinity (KCa = 0.22 μM; Kmax = 0.16 μmol/mg per min) and a low‐affinity (KCa = 148 μM; Vmax = 0.37 μtmol/mg per min) component. Calmodulin (0.12 μM) had no effect on Ca2+‐ATPase activity. However, trifluoperazine (0.1 mM), a calmodulin antagonist, strongly inhibited especially the high‐affinity component of the enzyme. Vanadate and lanthanum also caused inhibition. In the presence of CDTA, a potent Ca2+ and Mg2+ chelating agent, high‐affinity Ca2+‐ATPase activity was abolished, indicating that trace Mg2+ was essential for activity. The Ca2+‐ATPase substrate curve using ATP showed a high‐affinity (Km = 12.3 μM; Kmax= 0.022 μmol/mg per min) and a low‐affinity (Km = 43.8 μM; Vmax = 0.278 μmol/mg per min) component. These results demonstrate that osteoclasts have a plasma membrane Ca2+‐ATPase with characteristics similar to the enzyme responsible for active calcium extrusion in other cells.
Adult‐onset myopia and occupation

Abstract. Eleven female textile workers, all carrying out quality control on textiles (close‐working distance of 30 cm), were investigated with a view to refractive status. Eleven women in the same factory having other working tasks (office, sale, production) were used as a control group after being matched regarding age and education. Ninety percent of the close workers and 0% of the controls turned out to be myopic, and 80% of the close workers had no need for minus glasses before the age of 20 years. The refraction (in cycloplegia) was ‐2.56 (cases) vs +1.19 (controls). No deviation was observed concerning keratometry, anterior chamber depth and lens thickness. The axial length, however, was 24.36 mm and 22.72 mm, respectively.
DRAM failure analysis with the force-based scanning Kelvin probe

A fabrication induced failure in complementary metal-oxide-semiconductor dynamic random access memory (CMOS DRAM) cells has been imaged successfully with a novel combination of atomic force and scanning Kelvin probe microscopes. The imaging system was used to verify the presence, and subsequent removal of, ionic contaminants on a sub-micron scale.
Enhanced Use of Backup Pathways of NHEJ in G2 in Chinese Hamster Mutant Cells with Defects in the Classical Pathway of NHEJ

Abstract Wu, W. , Wang, M. , Mussfeldt, T. and Iliakis, G. Enhanced Use of Backup Pathways of NHEJ in G2 in Chinese Hamster Mutant Cells with Defects in the Classical Pathway of NHEJ. Radiat. Res. 170, 512–520 (2008). In higher eukaryotes DNA double-strand breaks (DSBs) are repaired by homologous recombination repair (HRR) or non-homologous end joining (NHEJ). In addition to the DNA-PK dependent pathway of NHEJ (D-NHEJ), cells employ a backup pathway (B-NHEJ) using DNA ligase III and PARP1. We have reported previously that mouse embryo fibroblasts (MEFs) defective in D-NHEJ show enhanced repair of DSBs in G2 not reflecting a contribution of HRR. Here we extend these studies to Chinese hamster mutant cells with defects in the DNA-PKcs, Ku80 or XRCC4 components of D-NHEJ or in the XRCC2 and XRCC3 components of HRR. Using cell sorting to separate cells at defined times after irradiation, we measure repair of DSBs with pulsed-field gel electrophoresis in unperturbed G1- and G2-phase cells. Wild-type cells and mutants of XRCC2 and XRCC3 repair DSBs with similar efficiency in G1 and G2. Mutants of DNA-PKcs, Ku80 and XRCC4 show more pronounced repair in G2 than in G1. These and previously published results provide support for the notion that the increased efficacy of DSB repair in G2 reflects the enhanced function of B-NHEJ, which may be a general feature of rodent cells that also holds for human cells.
Smells Are Sensitive to Developers! On the Efficiency of (Un)Guided Customized Detection

Code smells indicate poor implementation choices that may hinder program comprehension and maintenance. Their informal definition allows developers to follow different heuristics to detect smells in their projects. Machine learning has been used to customize smell detection according to the developer's perception. However, such customization is not guided (i.e. constrained) to consider alternative heuristics used by developers when detecting smells. As a result, their customization might not be efficient, requiring a considerable effort to reach high effectiveness. In fact, there is no empirical knowledge yet about the efficiency of such unguided approaches for supporting developer-sensitive smell detection. This paper presents Histrategy, a guided customization technique to improve the efficiency on smell detection. Histrategy considers a limited set of detection strategies, produced from different detection heuristics, as input of a customization process. The output of the customization process consists of a detection strategy tailored to each developer. The technique was evaluated in an experimental study with 48 developers and four types of code smells. The results showed that Histrategy is able to outperform six widely adopted machine learning algorithms – used in unguided approaches – both in effectiveness and efficiency. It was also confirmed that most developers benefit from using alternative heuristics to: (i) build their tailored detection strategies, and (ii) achieve efficient smell detection.
Apolipoprotein E‐deficient mice have an impaired immune response to Klebsiella pneumoniae

All lipoproteins are able to bind to bacterial lipopolysaccharide (LPS), thereby neutralizing its deleterious effects. However, we demonstrated, recently, that in the absence of apolipoprotein E (apoE), eight‐fold increased very‐low‐density lipoprotein levels were not sufficient to protect apoE‐deficient (apoE−/−) mice against LPS. During a live Gram‐negative infection, mechanisms other than LPS‐neutralization may play a role in the pathogenesis of the disease. In the present study we further examined the role of apoE in Gram‐negative sepsis.
The Relationship of Tamoxifen with Dementia, Depression, and Dependence in Activities of Daily Living in Elderly Nursing Home Residents

ABSTRACT Objectives. To evaluate the association between tamoxifen treatment and the prevalence of Alzheimer's disease, other dementias, depression, and the levels of dependence in activities of daily living (ADL) in elderly, nursing home residents. Participants. 93,031 women, at least 65 years old, whose data were part of the 1993 New York State MDS, and for whom there was documentation of treatment with at least one medication. Setting. New York State long-term care facilities. Design. Cross-sectional study via secondary analysis of 1,385 matched sets of residents. Each set included one resident who received tamoxifen treatment and up to four residents who did not. Measurements. Included age, ethnicity, tamoxifen treatment, hormone replacement therapy, depression, levels of dependence in ADL and in cognitive skills for daily decision-making, and documentation of Alzheimer's disease and other dementias. Results. Women receiving tamoxifen were less likely to have a diagnosis of Alzheimer's disease documented on the MDS (odds ratio: 0.674; 95% confidence interval: 0.551–0.823), were significantly more independent in bed mobility, eating, toileting (in each case P < 0.0001), personal hygiene (P = 0.0155), dressing (P = 0.0015), transferring (P = 0.0006), locomotion (P = 0.0016), and they had better cognitive skills for daily decision-making (P < 0.0001). They were, however, 42% more likely to have a MDS diagnosis of depression (P < 0.0001). All tests of statistical significance are two-sided. Conclusion. In this population, tamoxifen was associated with a higher level of independence in ADL and decision-making. While the MDS also suggested a relationship of tamoxifen with a lower prevalence of Alzheimer's disease, there seemed to be an increased prevalence of depression among treated women. The findings of this cross-sectional study could be evaluated in the randomized clinical trial that has just begun, and that will compare tamoxifen and raloxifene treatments.
Robust Explicit Time Optimal Controllers for Linear Systems via Decomposition Principle

Abstract One of the key problems in time optimal control (TOC) is the inherent computational complexity, which restricts its application to low dimensional systems. Considering a constrained linear system with bounded disturbances, this paper proposes a novel approach to reduce the computational complexity of TOC, where the terminal controller is nonlinear. It comprises several predetermined local linear feedback laws, resulting in a large terminal set. Starting from this relatively large terminal set, a large domain of attraction of the proposed TOC controller can be obtained by using a short horizon, and consequently leads to a low on-line computational effort. Furthermore, by formulating a suitable cost function, as time evolves, the TOC controller reaches the desired controller to obtain a good asymptotical behavior. The performance of the proposed approach is assessed via a numerical example.
Investigation on Single-Mode–Multimode– Single-Mode Fiber Structure

This paper presents an investigation on a single-mode-multimode-single-mode fiber structure. A one-way guided-mode propagation analysis for the circular symmetry waveguide is employed to model the light propagation and the approximated formulations are derived and evaluated concerning the accuracy. Phase conjunction of the multimode interference within the fiber structure is revealed. A simple way to predict and analyze the spectral response of the structure is presented through the space to wavelength mapping with the derived approximated formulations. The prediction of spectral response is verified numerically and experimentally.
Perspectives of Cell Therapy in Type 1 Diabetes

Type 1 diabetes is an autoimmune disease leading to the destruction of pancreatic cells. The reduction of cell mass results in insulin deficiency that leads to a failure of glucose homeostasis with increased levels of glucose in blood. Hyperglycemia which per se is detrimental for the organism and may be life-threatening, may in the long term associate with chronic complications involving blood vessels and nerves. The gold standard treatment for diabetes patients aimed to reach a tight control of glycemia, relies on intensive insulin therapy based on multiple daily injections or continuous subcutaneous infusion of insulin. A tight control of glycemia reached with such regimens was shown to significantly reduce the incidence of microvascular complications in respect to the conventional insulin therapy. Nevertheless, to reach an optimal control of blood levels may prove to be difficult when compared to the physiological condition where this is guaranteed by the pancreatic  cells (Suckale, 2008). Therefore, preservation of cell mass could be an important therapeutic target to reduce microvascular complications and to improve the glycemia control (Gonez & Knight, 2010). It is generally accepted that the endocrine pancreas has some regenerative capabilities, although it is still debated which cells are involved in cell turnover. In rodents the capability of adult pancreas to increase cell mass has been documented in physiological conditions and after injury. The understanding of mechanisms involved in  cell turnover may therefore be relevant to design new therapeutic strategies aimed to maintain a  cell mass or to favour regeneration of  cells. These strategies however, should take to account the problem of recurrent autoimmunity that in type 1 diabetes not only impairs the original cell mass, but may also limit the regenerative process. Indeed, autoimmune T lymphocytes may kill the cells newly formed in response to injury (Fan & Rudert, 2009).
Effects of land use on preferential flow paths distributions in southwestern China

Preferential flow plays an important role in the movement of soil water. Dye tracer experiments and computer image analysis were used to analyze morphological and distribution of preferential flow paths under different land uses (forest land, shrubs land, and farmland). The relationships between the preferential flow paths and root lengths, root holes and root surface area were analyzed by Pearson method. The results indicated that the upper 0–10 cm depth of the soil in all land uses had more than 50% dye coverage, and below 20 cm depth, the dye stained area was less than 30%. Preferential flow paths in soil are closely related to soil properties, root length, root holes, and root surface area. The soil properties in the area with preferential flow paths are quite different than that in soil matrix. The soil organic matter content was approximately 5–20% higher in the preferential flow paths area than that in the soil matrix. The percent of preferential flow paths in soil is significantly affected by roots with a diameter of less than 5 mm, root holes and root surface area. The vertical distribution is quite different in different land uses. Shrubs land and farmland have more preferential flow paths in the top soil layers than forestland, and the situation conversed in deeper soil layer.
Adjuvant chemotherapy with uracil-tegafur for pathological stage III rectal cancer after mesorectal excision with selective lateral pelvic lymphadenectomy: a multicenter randomized controlled trial.

BACKGROUND Although adjuvant radiotherapy was proved to be effective for local control of rectal cancer even after standardized mesorectal excision, the role of adjuvant chemotherapy after such standardized surgery remains to be clarified. We aimed to assess the efficacy of a combination of uracil and tegafur for pathological stage III rectal cancer treated by standardized mesorectal excision with selective lateral pelvic lymphadenectomy. METHODS We randomly assigned patients with completely resected stage III rectal cancer, who underwent standardized mesorectal excision with selective lateral pelvic lymphadenectomy, to receive either oral uracil-tegafur (400 mg/m2 tegafur per day) for one year or no treatment. Standardization and quality control of the surgery and pathological techniques were ensured by use of the guidelines of the Japanese Society for Cancer of the Colon and Rectum. The primary endpoint was relapse-free survival. The secondary endpoint was overall survival. RESULTS We enrolled and randomized 276 patients. Excluding two ineligible patients, 274 were included in the analysis. Planned interim analysis 2 years after accrual termination revealed significant prolongation of relapse-free survival (P = 0.001) and overall survival (P = 0.005) in the uracil-tegafur group. The 3-year relapse-free survival and overall survival rates were 78 and 91% in the chemotherapy group and 60 and 81% in the surgery-alone group, respectively. Local recurrence rates were low in both groups. Grade 3 events occurred in 17% of the chemotherapy patients, but no grade 4 or more events occurred. CONCLUSION Adjuvant chemotherapy with uracil-tegafur improves survival of patients with stage III rectal cancer after standardized mesorectal excision with selective lateral pelvic lymphadenectomy.
Ifosfamide is an active drug for chemotherapy of metastatic cystosarcoma phyllodes

Metastases from cystosarcoma phyllodes are rare, and treatment generally is ineffective. Four patients were treated with ifosfamide (alone in three and combined with doxorubicin in one). Two patients had complete remissions that lasted 26 and 61+ months. One other patient had a partial response that lasted 13 months. The complete responders were both treated as soon as metastases appeared, when they had only a small volume of disease. This appears to represent a significant improvement on other described regimens for this condition, and further trials of ifosfamide are warranted. Close follow‐up of patients at high risk for metastases is suggested.
Postnatal placental confirmation of trisomy 2 and trisomy 16 detected at chorionic villus sampling: A possible association with intrauterine growth retardation and elevated maternal serum alpha‐fetoprotein

Detection of trisomy 2 and trisomy 16 mosaicism through chorionic villus sampling (CVS) is not an infrequent finding. We describe here two cases, one of non‐mosaic trisomy 2 and the other of high level mosaicism for trisorny 16. Amniocentesis in both cases demonstrated non‐mosaic 46,XY karyotypes. Each pregnancy continued to delivery of liveborn, normal‐appearing boys; both pregnancies were complicated by severe intrauterine growth retardation (IUGR). Postnatal studies of placental biopsies in both cases confirmed the original CVS findings, whereas cord blood karyotypes were normal in both boys. Both children have demonstrated adequate catch‐up growth.