Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural network and genetic programming for modelling coastal algal blooms

In the recent past, machine learning (ML) techniques such as artificial neural networks (ANN) have been increasingly used to model algal bloom dynamics. In the present paper, along with ANN, we select genetic programming (GP) for modelling and prediction of algal blooms in Tolo Harbour, Hong Kong. The study of the weights of the trained ANN and also the GP-evolved equations shows that they correctly identify the ecologically significant variables. Analysis of various ANN and GP scenarios indicates that good predictions of long-term trends in algal biomass can be obtained using only chlorophyll-a as input. The results indicate that the use of biweekly data can simulate long-term trends of algal biomass reasonably well, but it is not ideally suited to give short-term algal bloom predictions.
Weight Loss and Lowering Androgens Predict Improvements in Health-Related Quality of Life in Women With PCOS.

CONTEXT Polycystic ovary syndrome (PCOS) is associated with reduced health-related quality of life (HRQOL) and increased prevalence of depressive and anxiety disorders. The impact of PCOS-specific treatments on these co-morbidities is unclear. OBJECTIVE To assess the impact of weight loss and decreasing hyperandrogenism on HRQOL and mood and anxiety disorders in women with PCOS. DESIGN/SETTING/PARTICIPANTS A secondary analysis of a randomized controlled trial (OWL-PCOS) of preconception treatment conducted at two academic centers in women (age, 18-40 years; body mass index, 27-42 kg/m(2)) with PCOS defined by Rotterdam criteria. INTERVENTION Continuous oral contraceptive pill (OCP) or intensive lifestyle intervention or the combination (Combined) for 16 weeks. MAIN OUTCOME MEASURE(S) Changes in HRQOL assessed by PCOSQ and SF-36 and prevalence of depression and anxiety disorder assessed by PRIME-MD PHQ. RESULTS The lowest scores were noted on the general health domain of the SF-36 and the weight and infertility domains on the PCOSQ. All three interventions resulted in significant improvement in the general health score on the SF-36. Both the OCP and Combined groups showed improvements in all domains of the PCOSQ (P < .01) compared to baseline scores. The Combined group had significant improvements in the weight, body hair, and infertility domains compared to a single treatment group (P < .05). In a linear regression model, change in weight correlated with improvements in the weight domain (P < .001) and physical well-being (P < .02), change in T correlated with improvements in the hair domain (P < .001), and change in both weight and T correlated with the infertility (P < .001) and menstrual domains (P < .05). CONCLUSIONS Both weight loss and OCP use result in significant improvements in several physical and mental domains related to quality of life, depressive symptoms, and anxiety disorders, and combined therapies offer further benefits in overweight/obese women with PCOS.
High‐resolution fast spin echo imaging of the human brain at 4.7 T: Implementation and sequence characteristics

In this work, a number of important issues associated with fast spin echo (FSE) imaging of the human brain at 4.7 T are addressed. It is shown that FSE enables the acquisition of images with high resolution and good tissue contrast throughout the brain at high field strength. By employing an echo spacing (ES) of 22 ms, one can use large flip angle refocusing pulses (162°) and a low acquisition bandwidth (50 kHz) to maximize the signal‐to‐noise ratio (SNR). A new method of phase encode (PE) ordering (called “feathering”) designed to reduce image artifacts is described, and the contributions of RF (B1) inhomogeneity, different echo coherence pathways, and magnetization transfer (MT) to FSE signal intensity and contrast are investigated. B1 inhomogeneity is measured and its effect is shown to be relatively minor for high‐field FSE, due to the self‐compensating characteristics of the sequence. Thirty‐four slice data sets (slice thickness = 2 mm; in‐plane resolution = 0.469 mm; acquisition time = 11 min 20 s) from normal volunteers are presented, which allow visualization of brain anatomy in fine detail. This study demonstrates that high‐field FSE produces images of the human brain with high spatial resolution, SNR, and tissue contrast, within currently prescribed power deposition guidelines. Magn Reson Med 51:1254–1264, 2004. © 2004 Wiley‐Liss, Inc.
Incremental , multi-level processing for comprehending situated dialogue in human-robot interaction

The article presents an implemented model for interpreting situated dialogue, as part of a system for human-robot interaction. The underlying assumption is that to understand situated dialogue, communicated meaning needs to be related to the situation(s) it refers to. The model couples incremental processing to a notion of bidirectional connectivity, inspired by how humans process visually situated language. Analyzing an utterance in a ”word-by-word, left-to-right” fashion, a representation of possible utterance interpretations is gradually built up. In a top-down fashion, the model tries to ground these interpretations in models the robot maintains of situations, through which they can prime what is focused on in a situation. In a bottom-up fashion, the (im)possibility to ground certain interpretations primes how the analysis of the utterance further unfolds. The article discusses the implementation of the model in a distributed, cognitive architecture for human-robot interaction, and presents an evaluation on a test suite.
Effects of Inhibition of Interleukin-6 Signalling on Insulin Sensitivity and Lipoprotein (A) Levels in Human Subjects with Rheumatoid Diseases

Background Interleukin-6 (IL-6) is a pro-inflammatory cytokine that has been found to be increased in type 2 diabetic subjects. However, it still remains unclear if these elevated IL-6 levels are co-incidental or if this cytokine is causally related to the development of insulin resistance and type 2 diabetes in humans. Therefore, in the present study we examined insulin sensitivity, serum adipokine levels and lipid parameters in human subjects before and after treatment with the IL-6 receptor antibody Tocilizumab. Methodology/Principal Findings 11 non-diabetic patients with rheumatoid disease were included in the study. HOMA-IR was calculated and serum levels for leptin, adiponectin, triglycerides, LDL-cholesterol, HDL-cholesterol and lipoprotein (a) (Lp (a)) were measured before as well as one and three months after Tocilizumab treatment. The HOMA index for insulin resistance decreased significantly. While leptin concentrations were not altered by inhibition of IL-6 signalling, adiponectin concentrations significantly increased. Thus the leptin to adiponectin ratio, a novel marker for insulin resistance, exhibited a significant decrease. Serum triglycerides, LDL-cholesterol and HDL-cholesterol tended to be increased whereas Lp (a) levels significantly decreased. Conclusions/Significance Inhibition of IL-6 signalling improves insulin sensitivity in humans with immunological disease suggesting that elevated IL-6 levels in type 2 diabetic subjects might be causally involved in the pathogenesis of insulin resistance. Furthermore, our data indicate that inhibition of IL-6 signalling decreases Lp (a) serum levels, which might reduce the cardiovascular risk of human subjects.
Effects of diluents on cell culture viability measured by automated cell counter

Commercially available automated cell counters based on trypan blue dye-exclusion are widely used in industrial cell culture process development and manufacturing to increase throughput and eliminate inherent variability in subjective interpretation associated with manual hemocytometers. When using these cell counters, sample dilution is often necessary to stay within the assay measurement range; however, the effect of time and diluents on cell culture is not well understood. This report presents the adverse effect of phosphate buffered saline as a diluent on cell viability when used in combination with an automated cell counter. The reduced cell viability was attributed to shear stress introduced by the automated cell counter. Furthermore, length of time samples were incubated in phosphate buffered saline also contributed to the observed drop in cell viability. Finally, as erroneous viability measurements can severely impact process decisions and product quality, this report identifies several alternative diluents that can maintain cell culture viability over time in order to ensure accurate representation of cell culture conditions.
The Impact of Community-Based Palliative Care on Utilization and Cost of Acute Care Hospital Services in the Last Year of Life.

BACKGROUND Community-based palliative care may potentially benefit patients by offering their preferred care at the end of life and benefit systems by reducing hospital use. OBJECTIVE To compare place of death and acute care hospital use in the last year of life between cancer decedents who did and did not access a community-based palliative care service (PCS). DESIGN Retrospective observational cohort study using linked individual administrative records from cancer registry, hospital, emergency department (ED), mortality, and PCS databases. Propensity score-weighted regression methods were used. SETTING/SUBJECTS Whole of population study incorporating 28,561 West Australian cancer decedents from 2001 to 2011. MEASUREMENTS Exposure was defined as ever/never accessed PCS. Outcomes were place of death (in/out of hospital) and the number, length of stay, and cumulative cost of hospital admissions at the end of life. RESULTS Decedents who accessed the service (n = 16,530) had triple (adjusted odds ratio 3.19 [3.01-3.38]) the odds of dying out of hospital compared with those who did not. Unplanned hospitalizations were reduced in the last year (adjusted incidence rate ratio [IRR] 0.94 [0.91-0.97]) and last week of life (adjusted [IRR] 0.35 [0.33-0.38]), as were ED presentations (adjusted RR 0.92 [0.98-0.95], adjusted RR 0.26 [0.23-0.28]) in the last year and last week of life, respectively. There were significant reductions in average total bed days (-7.60 [-8.34 to -6.87]) and acute care costs (-A$5,491 [-A$6,155 to -A$4,827]) over the last year of life. CONCLUSIONS In addition to supporting people to die out of hospital, PCS was associated with reduced acute care admissions, bed days, and costs over the last year of life. The provision of high-quality palliative care in the community alleviates the burden on acute care hospitals and, thus, may partially offset public funding of this model.
Delaying Caspase Activation by Bcl-2: A Clue to Disease Retardation in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis

Molecular mechanisms of apoptosis may participate in motor neuron degeneration produced by mutant copper/zinc superoxide dismutase (mSOD1), the only proven cause of amyotrophic lateral sclerosis (ALS). Consistent with this, herein we show that the spinal cord of transgenic mSOD1 mice is the site of the sequential activation of caspase-1 and caspase-3. Activated caspase-3 and its produced β-actin cleavage fragments are found in apoptotic neurons in the anterior horn of the spinal cord of affected transgenic mSOD1 mice; although such neurons are few, their scarcity should not undermine the potential importance of apoptosis in the overall mSOD1-related neurodegeneration. Overexpression of the anti-apoptotic protein Bcl-2 attenuates neurodegeneration and delays activation of the caspases and fragmentation of β-actin. These data demonstrate that caspase activation occurs in this mouse model of ALS during neurodegeneration. Our study also suggests that modulation of caspase activity may provide protective benefit in the treatment of ALS, a view that is consistent with our recent demonstration of caspase inhibition extending the survival of transgenic mSOD1 mice.
Prospective Study of JC Virus Seroreactivity and the Development of Colorectal Cancers and Adenomas

Background: Infection with JC virus has been proposed as a risk factor for colorectal cancer. A nested case-control study was conducted to evaluate the association between prediagnostic JC virus antibodies and the risk of incident colorectal cancer and adenomas. Methods: Two research serum banks were established in Washington County, MD in 1974 and 1989, with the collection of blood samples from >45,000 volunteers. Incident colorectal cancer cases diagnosed through 2006 (n = 611) were identified among participants by linkage to population-based cancer registries, contributing 729 pairs of observations. Cases of adenomatous polyps (n = 123) were identified from participants of the 1989 cohort who reported having a colonoscopy-detected adenoma at follow-up through 2000 with histology confirmed through medical record review. One control was matched to each case on age, sex, race, and date of blood draw, and, for adenoma controls, date of endoscopy. IgG antibodies to JC virus were measured using virus-like particle ELISA. Associations between JC virus seropositivity and colorectal cancer and adenomas were estimated using conditional logistic regression. Results: Overall, there was no association between antibodies to JC virus and colorectal cancer [odds ratio (OR), 0.91; 95% confidence interval (95% CI), 0.71-1.17]. However, a statistically significant positive association between JC virus seropositivity and subsequent adenoma diagnosis was observed among males (OR, 2.31; 95% CI, 1.20-4.46), whereas a statistically significant inverse association was observed among females (OR, 0.31; 95% CI, 0.14-0.67; P for interaction = 0.01), after adjustment for baseline smoking and body mass index. Conclusions: Overall, JC virus seropositivity was not associated with colorectal cancer development up to 31 years later. Future studies are needed to confirm the adenoma findings. (Cancer Epidemiol Biomarkers Prev 2009;18(5):1515–23)
Development of Full-Thickness Macular Hole despite Previous Posterior Vitreous Detachment and Vitrectomy for Retinal Detachment: Two Cases

Purpose To report the delayed development of idiopathic full-thickness macular hole in eyes with previously documented complete posterior vitreous detachment that were vitrectomized during surgery for rhegmatogenous retinal detachment. Methods Two interventional case reports with serial color fundus photographs and optical coherence tomography scans. Results Case 1: A 62-year-old man underwent vitrectomy cryoretinopexy and intraocular gas tamponade for rhegmatogenous retinal detachment associated with a complete posterior vitreous detachment. Three years later, he developed a full-thickness macular hole in the same eye. Peeling of the inner limiting membrane and gas tamponade resulted in complete closure of the macular hole with improvement in visual acuity. Case 2: A 70-year-old man presented with a macula-off inferior retinal detachment and counting fingers vision. Vitrectomy cryoretinopexy to a single tear, and gas tamponade was successful and acuity improved to 6/9. He subsequently developed retinal redetachment associated with a new retinal tear and was treated by further vitrectomy and gas. He developed a full-thickness macular hole in the same eye 2 years later with acuity dropping to 1/60. Conclusions Macular hole formation may occur in the context of vitrectomized eyes. These observations support the hypothesis that anteroposterior vitreomacular traction, while traditionally implicated, is not always essential for the development of macular holes.
tRNA Methyltransferase Homolog Gene TRMT10A Mutation in Young Onset Diabetes and Primary Microcephaly in Humans

We describe a new syndrome of young onset diabetes, short stature and microcephaly with intellectual disability in a large consanguineous family with three affected children. Linkage analysis and whole exome sequencing were used to identify the causal nonsense mutation, which changed an arginine codon into a stop at position 127 of the tRNA methyltransferase homolog gene TRMT10A (also called RG9MTD2). TRMT10A mRNA and protein were absent in lymphoblasts from the affected siblings. TRMT10A is ubiquitously expressed but enriched in brain and pancreatic islets, consistent with the tissues affected in this syndrome. In situ hybridization studies showed that TRMT10A is expressed in human embryonic and fetal brain. TRMT10A is the mammalian ortholog of S. cerevisiae TRM10, previously shown to catalyze the methylation of guanine 9 (m1G9) in several tRNAs. Consistent with this putative function, in silico topology prediction indicated that TRMT10A has predominant nuclear localization, which we experimentally confirmed by immunofluorescence and confocal microscopy. TRMT10A localizes to the nucleolus of β- and non-β-cells, where tRNA modifications occur. TRMT10A silencing induces rat and human β-cell apoptosis. Taken together, we propose that TRMT10A deficiency negatively affects β-cell mass and the pool of neurons in the developing brain. This is the first study describing the impact of TRMT10A deficiency in mammals, highlighting a role in the pathogenesis of microcephaly and early onset diabetes. In light of the recent report that the type 2 diabetes candidate gene CDKAL1 is a tRNA methylthiotransferase, the findings in this family suggest broader relevance of tRNA methyltransferases in the pathogenesis of type 2 diabetes.
Angiopoietin-2 levels are associated with retinopathy and predict mortality in Malawian children with cerebral malaria: A retrospective case–control study*

Objective:To investigate the relationship among the angiopoietin–Tie-2 system, retinopathy, and mortality in children with cerebral malaria. Design:A case–control study of retinopathy-positive vs. retinopathy-negative children with clinically defined cerebral malaria. Setting:Queen Elizabeth Central Hospital in Blantyre, Malawi. Subjects:One hundred fifty-five children presenting with severe malaria and meeting a strict definition of clinical cerebral malaria (Blantyre Coma Score ⩽2, Plasmodium falciparum parasitemia, no other identifiable cause for coma) were included in the study. Interventions:None. Measurements and Main Results:Clinical and laboratory parameters were recorded at admission and funduscopic examinations were performed. Admission levels of angiopoietin-1, angiopoietin-2, and a soluble version of their cognate receptor were measured by enzyme-linked immunosorbent assay. We show that angiopoietin-1 levels are decreased and angiopoietin-2 and soluble Tie-2 levels are increased in children with cerebral malaria who had retinopathy compared with those who did not. Angiopoietin-2 and soluble Tie-2 were independent predictors of retinopathy (adjusted odds ratio [95% CI], angiopoietin-2, 4.3 [1.3–14.6], p = .019; soluble Tie-2, 9.7 [2.1–45.8], p = .004). Angiopoietin-2 and soluble Tie-2 were positively correlated with the number of hemorrhages, the severity or retinal whitening, and the extent of capillary whitening observed on funduscopic examination (p < .05 after adjustment for multiple comparisons). Angiopoietin-2 and soluble Tie-2 levels were elevated in children with cerebral malaria who subsequently died and angiopoetin-2 was an independent predictor of death (adjusted odds ratio: 3.9 [1.2–12.7], p = .024). When combined with clinical parameters, angiopoetin-2 improved prediction of mortality using logistic regression models and classification trees. Conclusions:These results provide insights into mechanisms of endothelial activation in cerebral malaria and indicate that the angiopoietin–Tie-2 axis is associated with retinopathy and mortality in pediatric cerebral malaria.
The Effects of Apprenticeship of Observation on Teachers Attitudes towards Active Learning Instruction

Kuzhabekova Aliya - PhD in Higher Education Policy and Administration (University of Minnesota, USA); Assistant Professor, Graduate School of Education, Nazarbayev University (Kazakhstan). E-mail address: aliya.kuzhabekova@nu.edu. kz Zhaparova Raina - Master of Science in Investment Banking and Finance (Glasgow University, U K); Teacher of Economics and Social Studies at Nazarbayev Intellectual School of Astana city. E-mail address: raina.zhaparova@nu.edu. kz Address: 53 Kabanbay Batyr Avenue, 010000, Astana, Kazakhstan.Active learning instruction is promoted by the most recent version of the National Program for the Development of Education in Kazakhstan as it is believed to provide more meaningful learning and deeper understanding compared to traditional instruction. In order to achieve greater utilization of the instructional approach at schools, teachers must be aware of active learning techniques and know how to use them. The paper studies whether apprenticeship of observation" during a graduate course using active learning techniques had an impact on novice and experienced teachers" attitudes towards active learning instruction. The study used data from a survey of students taking the course, which was focused on educational issues rather than methodologi cal training. The results of the study confirmed the hypotheses that apprenticeship of observation" has an influence on teachers not only during pre-service training, but also at later stages of their careers, when they become involved in professional development or continuing education. This influence was especially obvious for teachers with no or little exposure to professional development. Based on these results the paper also suggests some practical implications. Limitations and biases that could affect results are also mentioned.DOI: 10.17323/1814-9545-2016-2-208-228
Ancillary Care in South African HIV Vaccine Trials: Addressing Needs, Drafting Protocols, and Engaging Community

There has been debate about sponsor-investigator ethical responsibilities to address participants' medical needs in trials in resource-constrained contexts. Certain ethical guidelines make detailed recommendations. This study explored whether ethical guideline recommendations for care in HIV vaccine trials were being met, and whether stakeholders were facing difficulties addressed by guidelines. It sampled key stakeholders involved in two trials across five sites in South Africa, and reviewed relevant documentation. It concluded that sites were largely meeting guideline recommendations for addressing needs, with some exceeding these. Recommendations for writing protocols were only partially achieved. Recommendations for engaging participating community were mostly met, except for “moral negotiation” recommendations. Suggestions are made to strengthen practices, and to improve guidelines so they address empirical concerns.
Fast lookup for dynamic packet filtering in FPGA

Rapidly growing speed and complexity of computer networks impose new requirements on fast lookup structures which are utilized in many networking applications (SDN, firewalls, NATs, etc.). We propose a novel lookup concept based on the well-known cuckoo hashing, which can achieve good memory utilization, supplemented by a binary search tree for offloading the colliding keys and supporting LPM lookup. We also propose a hardware architecture implementing this lookup concept in the FPGA. Our solution is suitable for lookup of the variable-length keys in 100+ Gbps networks. Memory utilization of the proposed concept is thoroughly evaluated and it is shown that the concept is scalable to external memory components.