Miracle-dz/UniFAR-FTUs huggingface dataset:
CCG Supertags in Factored Statistical Machine Translation

Combinatorial Categorial Grammar (CCG) supertags present phrase-based machine translation with an opportunity to access rich syntactic information at a word level. The challenge is incorporating this information into the translation process. Factored translation models allow the inclusion of supertags as a factor in the source or target language. We show that this results in an improvement in the quality of translation and that the value of syntactic supertags in flat structured phrase-based models is largely due to better local reorderings.
Real-time semi-global dense stereo solution with improved sub-pixel accuracy

In this work we focus on creating a real-time dense stereo reconstruction system with accurate sub-pixel estimation. We selected the Semi-Global Matching method as the basis of our system due to its high quality and possible real-time implementations. In our solution we use the Census transform as the matching metric because our results show that it can reduce the matching errors for traffic images compared to classical solutions. We also propose several modifications to the original Semi-Global algorithm to improve the sub-pixel accuracy and the execution time. One of these proposals is the reduction in the number of optimization directions without affecting the results. The second modification is a correction of the energy function to reduce the spread of depth values. Besides these improvements, the paper also introduces a new aggregation method used to reduce the spread of sub-pixel values. Finally we propose a new method to generate sub-pixel interpolation functions based on real-world data. The result of these enhancements is a significant improvement in sub-pixel accuracy. The system was implemented and evaluated on a current generation GPU with a running time of 19ms for image having the resolution 512×383.
Experimental evolution of protozoan traits in response to interspecific competition

Decades of experiments have demonstrated the ecological effect of competition, but experimental evidence for competitive effects on trait evolution is rare. I measured the evolution of six protozoan traits in response to competitors from the inquiline community of pitcher plants. Replicate populations of Colpoda, a ciliated protozoan, were allowed to evolve in response to intra‐ and interspecific competition for 20 days (approximately 100 generations), before traits were measured in two common garden environments. Populations that evolved with interspecific competition had smaller cell sizes, produced fewer cysts and had higher population growth rates relative to populations grown in monoculture. The presence of interspecific competitors led to differential lineage sorting, most likely by increasing the strength of selection. These results are the first to demonstrate protozoan evolution in response to competition and may have implications for species coexistence in this system.
Transendocardial, Autologous Bone Marrow Cell Transplantation for Severe, Chronic Ischemic Heart Failure

Background—This study evaluated the hypothesis that transendocardial injections of autologous mononuclear bone marrow cells in patients with end-stage ischemic heart disease could safely promote neovascularization and improve perfusion and myocardial contractility. Methods and Results—Twenty-one patients were enrolled in this prospective, nonrandomized, open-label study (first 14 patients, treatment; last 7 patients, control). Baseline evaluations included complete clinical and laboratory evaluations, exercise stress (ramp treadmill), 2D Doppler echocardiogram, single-photon emission computed tomography perfusion scan, and 24-hour Holter monitoring. Bone marrow mononuclear cells were harvested, isolated, washed, and resuspended in saline for injection by NOGA catheter (15 injections of 0.2 cc). Electromechanical mapping was used to identify viable myocardium (unipolar voltage ≥6.9 mV) for treatment. Treated and control patients underwent 2-month noninvasive follow-up, and treated patients alone underwent a 4-month invasive follow-up according to standard protocols and with the same procedures used as at baseline. Patient population demographics and exercise test variables did not differ significantly between the treatment and control groups; only serum creatinine and brain natriuretic peptide levels varied in laboratory evaluations at follow-up, being relatively higher in control patients. At 2 months, there was a significant reduction in total reversible defect and improvement in global left ventricular function within the treatment group and between the treatment and control groups (P =0.02) on quantitative single-photon emission computed tomography analysis. At 4 months, there was improvement in ejection fraction from a baseline of 20% to 29% (P =0.003) and a reduction in end-systolic volume (P =0.03) in the treated patients. Electromechanical mapping revealed significant mechanical improvement of the injected segments (P <0.0005) at 4 months after treatment. Conclusions—Thus, the present study demonstrates the relative safety of intramyocardial injections of bone marrow–derived stem cells in humans with severe heart failure and the potential for improving myocardial blood flow with associated enhancement of regional and global left ventricular function.
Ultrastructure of GABA- and Tachykinin-Immunoreactive Neurons in the Lower Division of the Central Body of the Desert Locust

The central complex, a group of neuropils spanning the midline of the insect brain, plays a key role in spatial orientation and navigation. In the desert locust and other species, many neurons of the central complex are sensitive to the oscillation plane of polarized light above the animal and are likely involved in the coding of compass directions derived from the polarization pattern of the sky. Polarized light signals enter the locust central complex primarily through two types of γ-aminobutyric acid (GABA)-immunoreactive tangential neurons, termed TL2 and TL3 that innervate specific layers of the lower division of the central body (CBL). Candidate postsynaptic partners are columnar neurons (CL1) connecting the CBL to the protocerebral bridge (PB). Subsets of CL1 neurons are immunoreactive to antisera against locustatachykinin (LomTK). To better understand the synaptic connectivities of tangential and columnar neurons in the CBL, we studied its ultrastructural organization in the desert locust, both with conventional electron microscopy and in preparations immunolabeled for GABA or LomTK. Neuronal profiles in the CBL were rich in mitochondria and vesicles. Three types of vesicles were distinguished: small clear vesicles with diameters of 20–40 nm, dark dense-core vesicles (diameter 70–120 nm), and granular dense-core vesicles (diameter 70–80 nm). Neurons were connected via divergent dyads and, less frequently, through convergent dyads. GABA-immunoreactive neurons contained small clear vesicles and small numbers of dark dense core vesicles. They had both pre- and postsynaptic contacts but output synapses were observed more frequently than input synapses. LomTK immunostaining was concentrated on large granular vesicles; neurons had pre- and postsynaptic connections often with neurons assumed to be GABAergic. The data suggest that GABA-immunoreactive tangential neurons provide signals to postsynaptic neurons in the CBL, including LomTK-immunolabeled CL1 neurons, but in addition also receive input from LomTK-labeled neurons. Both types of neuron are additionally involved in local circuits with other constituents of the CBL.
The Single Dynamin Family Protein in the Primitive Protozoan Giardia lamblia Is Essential for Stage Conversion and Endocytic Transport

Dynamins are universally conserved large guanosine triphosphatases, which function as mechanoenzymes in membrane scission. The primitive protozoan Giardia lamblia has a single dynamin‐related protein (GlDRP) with an unusual domain structure. Giardia lacks a Golgi apparatus but generates transient Golgi‐like delay compartments dubbed encystation‐specific vesicles (ESVs), which serve to accumulate and mature cyst wall proteins during differentiation to infectious cyst forms. Here, we analyze the function of GlDRP during growth and encystation and demonstrate that it relocalizes from peripheral endosomal–lysosomal compartments to nascent ESVs. We show that GlDRP is necessary for secretion of the cyst wall material and ESV homeostasis. Expression of a dominant‐negative GlDRP variant does not interfere with ESV formation but blocks cyst formation completely prior to regulated exocytosis. GlDRP colocalizes with clathrin at the cell periphery and is necessary for endocytosis of surface proteins to endosomal–lysosomal organelles in trophozoites. Electron microscopy and live cell imaging reveal gross morphological changes as well as functional impairment of the endocytic system in cells expressing the dominant‐negative GlDRP. Thus, giardial DRP plays a key role in two distinct trafficking pathways and in organelle homeostasis, both essential functions for the proliferation of the parasite in the gut and its transmission to a new host.
Modulation of Mucosal Immune Response, Tolerance, and Proliferation in Mice Colonized by the Mucin-Degrader Akkermansia muciniphila

Epithelial cells of the mammalian intestine are covered with a mucus layer that prevents direct contact with intestinal microbes but also constitutes a substrate for mucus-degrading bacteria. To study the effect of mucus degradation on the host response, germ-free mice were colonized with Akkermansia muciniphila. This anaerobic bacterium belonging to the Verrucomicrobia is specialized in the degradation of mucin, the glycoprotein present in mucus, and found in high numbers in the intestinal tract of human and other mammalian species. Efficient colonization of A. muciniphila was observed with highest numbers in the cecum, where most mucin is produced. In contrast, following colonization by Lactobacillus plantarum, a facultative anaerobe belonging to the Firmicutes that ferments carbohydrates, similar cell-numbers were found at all intestinal sites. Whereas A. muciniphila was located closely associated with the intestinal cells, L. plantarum was exclusively found in the lumen. The global transcriptional host response was determined in intestinal biopsies and revealed a consistent, site-specific, and unique modulation of about 750 genes in mice colonized by A. muciniphila and over 1500 genes after colonization by L. plantarum. Pathway reconstructions showed that colonization by A. muciniphila altered mucosal gene expression profiles toward increased expression of genes involved in immune responses and cell fate determination, while colonization by L. plantarum led to up-regulation of lipid metabolism. These indicate that the colonizers induce host responses that are specific per intestinal location. In conclusion, we propose that A. muciniphila modulates pathways involved in establishing homeostasis for basal metabolism and immune tolerance toward commensal microbiota.
Cost-Effectiveness of Coronary Artery Calcium Testing for Coronary Heart and Cardiovascular Disease Risk Prediction to Guide Statin Allocation: The Multi-Ethnic Study of Atherosclerosis (MESA)

Background The Multi-Ethnic Study of Atherosclerosis (MESA) showed that the addition of coronary artery calcium (CAC) to traditional risk factors improves risk classification, particularly in intermediate risk asymptomatic patients with LDL cholesterol levels <160 mg/dL. However, the cost-effectiveness of incorporating CAC into treatment decision rules has yet to be clearly delineated. Objective To model the cost-effectiveness of CAC for cardiovascular risk stratification in asymptomatic, intermediate risk patients not taking a statin. Treatment based on CAC was compared to (1) treatment of all intermediate-risk patients, and (2) treatment on the basis of United States guidelines. Methods We developed a Markov model of first coronary heart disease (CHD) and cardiovascular disease (CVD) events. We modeled statin treatment in intermediate risk patients with CAC≥1 and CAC≥100, with different intensities of statins based on the CAC score. We compared these CAC-based treatment strategies to a “treat all” strategy and to treatment according to the Adult Treatment Panel III (ATP III) guidelines. Clinical and economic outcomes were modeled over both five- and ten-year time horizons. Outcomes consisted of CHD and CVD events and Quality-Adjusted Life Years (QALYs). Sensitivity analyses considered the effect of higher event rates, different CAC and statin costs, indirect costs, and re-scanning patients with incidentalomas. Results We project that it is both cost-saving and more effective to scan intermediate-risk patients for CAC and to treat those with CAC≥1, compared to treatment based on established risk-assessment guidelines. Treating patients with CAC≥100 is also preferred to existing guidelines when we account for statin side effects and the disutility of statin use. Conclusion Compared to the alternatives we assessed, CAC testing is both effective and cost saving as a risk-stratification tool, particularly if there are adverse effects of long-term statin use. CAC may enable providers to better tailor preventive therapy to patients' risks of CVD.
Vitamin D supplementation reduces insulin resistance in South Asian women living in New Zealand who are insulin resistant and vitamin D deficient – a randomised, placebo-controlled trial

Low serum 25-hydroxyvitamin D (25(OH)D) has been shown to correlate with increased risk of type 2 diabetes. Small, observational studies suggest an action for vitamin D in improving insulin sensitivity and/or insulin secretion. The objective of the present study was to investigate the effect of improved vitamin D status on insulin resistance (IR), utilising randomised, controlled, double-blind intervention administering 100 μg (4000 IU) vitamin D3 (n 42) or placebo (n 39) daily for 6 months to South Asian women, aged 23–68 years, living in Auckland, New Zealand. Subjects were insulin resistant – homeostasis model assessment 1 (HOMA1)>1·93 and had serum 25(OH)D concentration < 50 nmol/l. Exclusion criteria included diabetes medication and vitamin D supplementation >25 μg (1000 IU)/d. The HOMA2 computer model was used to calculate outcomes. Median (25th, 75th percentiles) serum 25(OH)D3 increased significantly from 21 (11, 40) to 75 (55, 84) nmol/l with supplementation. Significant improvements were seen in insulin sensitivity and IR (P = 0·003 and 0·02, respectively), and fasting insulin decreased (P = 0·02) with supplementation compared with placebo. There was no change in C-peptide with supplementation. IR was most improved when endpoint serum 25(OH)D reached ≥ 80 nmol/l. Secondary outcome variables (lipid profile and high sensitivity C-reactive protein) were not affected by supplementation. In conclusion, improving vitamin D status in insulin resistant women resulted in improved IR and sensitivity, but no change in insulin secretion. Optimal vitamin D concentrations for reducing IR were shown to be 80–119 nmol/l, providing further evidence for an increase in the recommended adequate levels. Registered Trial No. ACTRN12607000642482.
Structure of O-Antigen and Hybrid Biosynthetic Locus in Burkholderia cenocepacia Clonal Variants Recovered from a Cystic Fibrosis Patient

Burkholderia cenocepacia is an opportunistic pathogen associated with chronic lung infections and increased risk of death in patients with cystic fibrosis (CF). In this work, we investigated the lipopolysaccharide (LPS) of clinical variants of B. cenocepacia that were collected from a CF patient over a period of 3.5 years, from the onset of infection until death by necrotizing pneumonia (cepacia syndrome). We report the chemical structure of the LPS molecule of various sequential isolates and the identification of a novel hybrid O-antigen (OAg) biosynthetic cluster. The OAg repeating unit of the LPS from IST439, the initial isolate, is a [→2)-β-D-Ribf-(1→4)-α-D-GalpNAc-(1→] disaccharide, which was not previously described in B. cenocepacia. The IST439 OAg biosynthetic gene cluster contains 7 of 23 genes that are closely homologous to genes found in B. multivorans, another member of the Burkholderia cepacia complex. None of the subsequent isolates expressed OAg. Genomic sequencing of these isolates enabled the identification of mutations within the OAg cluster, but none of these mutations could be associated with the loss of OAg. This study provides support to the notion that OAg LPS modifications are an important factor in the adaptation of B. cenocepacia to chronic infection and that the heterogeneity of OAgs relates to variation within the OAg gene cluster, indicating that the gene cluster might have been assembled through multiple horizontal transmission events.
Patterns of bee and butterfly diversity in Southeast and Southern East Asian megacities / Sing Kong Wah

I investigated bee diversity and human perceptions of bees in four megacities – Greater Bangkok, Klang Valley, Pearl River Delta, and Singapore-Iskandar Malaysia. I sampled bees and conducted questionnaires at three different site types in each megacity: a botanical garden, central business district and peripheral suburban areas. Overall, the mean species richness and abundance of bees were significantly higher in peripheral suburban areas than central business districts (p < 0.05). Urban residents were unlikely to have seen bees but agreed that bees have a right to exist in their natural environment. Residents who did notice and interact with bees, were more likely to have positive opinions towards the presence of bees in cities. Additionally, I examined the species diversity of butterflies in urban parks in two cities ─ the Federal Territory of Kuala Lumpur, Malaysia and Shenzhen, South China. I investigated the relationships between butterfly species richness and three park variables: i) park age, ii) park size and iii) distance from the central business district. I conducted standardized butterfly sampling across different microhabitat types at each park: i) groves, ii) hedges, iii) flowerbeds and iv) unmanaged areas. I recorded 572 butterflies belonging to 60 species in Kuala Lumpur‟s urban parks. Although species richness was positively correlated with park age and size and negatively correlated with distance from the central business district; the correlations were not statistically significant. The highest species richness was recorded in the unmanaged microhabitat. In Shenzhen, I collected 1933 butterflies belonging to 74 species. Butterfly species richness showed weak negative correlations with park age and distance from the central business district but the positive correlation with park size was statistically significant (p < 0.05). Among microhabitat types, highest species richness was recorded in unmanaged areas.
The crystallisation of Poly (aryl ether etherketone) (PEEK) and its carbon fibre composites

Thermoplastic matrix composites are advantageous over thermosetting matrix composites in that they can give improved damage tolerance, shorter production times and inherent recyclability (via melt reprocessing). Poly aryl ether ether ketone (PEEK) is a semi-crystalline, high-performance engineering polymer whose properties can be enhanced through fibre reinforcement. The properties of PEEK and its composites are sensitive to changes in the crystalline content and morphology, which are influenced by the processing conditions. As such it is of great importance to have a good understanding of the crystallisation process of PEEK under various conditions. A number of parameters were investigated with respect to their effects on the crystallisation of neat and carbon fibre reinforced PEEK. The parameters studied were the melt temperature, the isothermal crystallisation temperature, and the non-isothermal cooling rate. It is of paramount importance to heat PEEK in excess of 400°C before processing to remove all previous crystalline entities. PEEK crystallises more rapidly in the presence of carbon fibres as a result of heterogeneous nucleation at the fibre surface. PEEK crystallises in the form of spherulitic crystals under isothermal crystallisation conditions. An increased cooling rate lowers the degree of crystallinity of PEEK as calculated by DSC and verified indirectly by FTIR.
Evidence levels for publications in pathology and laboratory medicine.

The standardization of various medical procedures, an evaluation of “quality” care, and the development of formal approaches to error prevention are becoming increasingly important processes in modern medicine.1 Procedural and interpretative algorithms, evidence-based practice protocols, and other guidelines have been published by various medical societies, and others are sure to follow.2 Compliance with their use is usually regarded as a “yardstick” for quality evaluation by health care administrators, and such information is used by payers and licensing agencies; it is even electronically published on the Internet.3 Accordingly, most medical specialties currently sponsor the development of “evidence-based” practice guidelines that are developed by using various concepts that fall under the rubric of “evidence-based medicine” (EBM). 4 As a group, however, pathologists have been slow to adopt a similar approach, which can be termed evidence-based pathology . 5,6 Literally hundreds of evidence-based medical protocols are already readily available through the National Guideline Clearinghouse, the Institute of Medicine, the American Cancer Society, the Cochrane Collaboration, and other Web sites.2,7–9 These documents are based on data in medical publications, which are generally referenced as …
Morphometric Study of Foramen Magnum and Variation in Its Shape

Introduction: Foramen magnum plays an important role as a landmark in the region of skull and spine because it transmits key structures like the lower end of the medulla oblongata, meninges, vertebral arteries and the spinal accessory nerve. Aims and objectives: Our aim was to provide basic osteometric data of anteroposterior and transverse diameters of foramen magnum and to observe its different shapes. Materials and methods: Thirty Four (34) adult human skulls of unknown sex were obtained from Department of Anatomy, RIMS, Ranchi. Foramen magnum diameters were calculated using sliding vernier calipers and shapes were visually assessed. Observations and results: Maximum anteroposterior diameter of foramen magnum was found to be 41.5mm and minimum was 28.5mm with the mean of 34.06mm whereas Maximum transverse diameter was 35mm and minimum was 22mm with the mean of 27.83mm. Percentage of foramen magnum shapes were as follows: oval 58.8%, Tetragonal 17.6%, hexagonal 11.8%, circular 8.82% and irregular 2.94% cases. Conclusion: Knowledge of dimensions of foramen magnum is important for radiologist, orthopaedicians and neurosurgeons, while planning and performing cranio-vertebral junction surgeries.