Miracle-dz/UniFAR-FTUs huggingface dataset:
LDA*: A Robust and Large-scale Topic Modeling System

We present LDA*, a system that has been deployed in one of the largest Internet companies to fulfil their requirements of "topic modeling as an internal service"---relying on thousands of machines, engineers in different sectors submit their data, some are as large as 1.8TB, to LDA* and get results back in hours. LDA* is motivated by the observation that none of the existing topic modeling systems is robust enough---Each of these existing systems is designed for a specific point in the tradeoff space that can be sub-optimal, sometimes by up to 10×, across workloads. Our first contribution is a systematic study of all recently proposed samplers: AliasLDA, F+LDA, LightLDA, and WarpLDA. We discovered a novel system tradeoff among these samplers. Each sampler has different sampling complexity and performs differently, sometimes by 5×, on documents with different lengths. Based on this tradeoff, we further developed a hybrid sampler that uses different samplers for different types of documents. This hybrid approach works across a wide range of workloads and outperforms the fastest sampler by up to 2x. We then focused on distributed environments in which thousands of workers, each with different performance (due to virtualization and resource sharing), coordinate to train a topic model. Our second contribution is an asymmetric parameter server architecture that pushes some computation to the parameter server side. This architecture is motivated by the skew of the word frequency distribution and a novel tradeoff we discovered between communication and computation. With this architecture, we outperform the traditional, symmetric architecture by up to 2×. With these two contributions, together with a carefully engineered implementation, our system is able to outperform existing systems by up to 10× and has already been running to provide topic modeling services for more than six months.
Pipa: pipelined profiling and analysis on multi-core systems

Dynamic instrumentation systems are gaining popularity as means of constructing customized program profiling and analysis tools. However, dynamic instrumentation based analysis tools still suffer from performance problems. The overhead of such systems can be broken down into two components - the overhead of dynamic instrumentation and the time consumed in the user-defined analysis tools. While important progress has been made in reducing the performance penalty of the dynamic instrumentation itself, less attention has been paid to the user-defined component. In this paper, we present PiPA - Pipelined Profiling and Analysis, which is a novel technique for parallelizing dynamic program profiling and analysis by taking advantage of multi-core systems. We implemented a prototype of PiPA using the dynamic instrumentation system DynamoRIO. Our experiments show that PiPA is able to speed up the overall profiling and analysis tasks significantly. Compared to the more than 100x slowdown of Cachegrind and the 32x slowdown of Pin dcache, we achieved a mere 10.5x slowdown on an 8-core system.
The Effect of Opioid Receptor Blockade on the Neural Processing of Thermal Stimuli

The endogenous opioid system represents one of the principal systems in the modulation of pain. This has been demonstrated in studies of placebo analgesia and stress-induced analgesia, where anti-nociceptive activity triggered by pain itself or by cognitive states is blocked by opioid antagonists. The aim of this study was to characterize the effect of opioid receptor blockade on the physiological processing of painful thermal stimulation in the absence of cognitive manipulation. We therefore measured BOLD (blood oxygen level dependent) signal responses and intensity ratings to non-painful and painful thermal stimuli in a double-blind, cross-over design using the opioid receptor antagonist naloxone. On the behavioral level, we observed an increase in intensity ratings under naloxone due mainly to a difference in the non-painful stimuli. On the neural level, painful thermal stimulation was associated with a negative BOLD signal within the pregenual anterior cingulate cortex, and this deactivation was abolished by naloxone.
Visceromotor Organization within Descending Spinal Sympathetic Pathways in the Dog

The organization within the descending sympathetic pathways on the surface of the dorsolateral funiculus of the spinal cord was investigated in anesthetized dogs. Changes in heart rate and carotid, renal, and femoral resistances were calculated during electrical stimulation of the descending spinal sympathetic pathways; the location within the pathway of the maximum change in each of these parameters was then determined. Blood pressure increased at each stimulation point with the maximum increase at 3–3.5 mm ventrolateral to the dorsolateral sulcus (DLS). The maximum increases in carotid, renal, and femoral resistances occurred with stimulation at 0.5–1.5, 2, and 3 mm ventrolateral to the DLS, respectively. Maximum heart rate responses were elicited by stimulation 2 mm ventrolateral to the sulcus. These data demonstrate that the pathway is organized in a dorsal-to-ventral manner, with the most rostral parts of the body being represented most dorsally and the more caudal parts being represented more ventrally.
Comparative mRNA Expression Profiles of Riboflavin Biosynthesis Genes in Lactobacilli Isolated from Human Feces and Fermented Bamboo Shoots

With the aim to bioprospect potent riboflavin producing lactobacilli, the present study was carried out to evaluate the relative mRNA expression of riboflavin biosynthesis genes namely Rib 1, Rib 2, Rib 3, and Rib 4 from potent riboflavin producers obtained from our previous studies. All the four genes were successfully cloned and sequenced for further analysis by in silico procedures. As studied by non-denaturing Polyacrylamide gel electrophoresis, no difference in size of all the four genes among those of various lactobacilli was observed. The relative fold increase in mRNA expression in Rib 1, Rib 2, Rib 3, and Rib 4 genes has been observed to be 10-, 1-, 0.7-, and 8.5-fold, respectively. Due to increase in relative mRNA expression for all the Rib genes as well as phenotypic production attribute, KTLF1 strain was used further for expression studies in milk and whey. The fold increase in mRNA expression for all the four Rib genes was higher at 12 and 18 h in milk and whey respectively. After exposure to roseoflavin, resistant variant of KTLF1 showed considerable increase in expression of all the targets genes. This is the first ever study to compare the mRNA expression of riboflavin biosynthesis pathway genes in lactobacilli and it also under lines the effect of media and harvesting time which significantly affect the expression of rib genes. The use of roseoflavin-resistant strains capable of synthesizing riboflavin in milk and whey paves a way for an exciting and economically viable biotechnological approach to develop novel riboflavin bio-enriched functional foods.
Unknown Word Extraction for Chinese Documents

There is no blank to mark word boundaries in Chinese text. As a result, identifying words is difficult, because of segmentation ambiguities and occurrences of unknown words. Conventionally unknown words were extracted by statistical methods because statistical methods are simple and efficient. However the statistical methods without using linguistic knowledge suffer the drawbacks of low precision and low recall, since character strings with statistical significance might be phrases or partial phrases instead of words and low frequency new words are hardly identifiable by statistical methods. In addition to statistical information, we try to use as much information as possible, such as morphology, syntax, semantics, and world knowledge. The identification system fully utilizes the context and content information of unknown words in the steps of detection process, extraction process, and verification process. A practical unknown word extraction system was implemented which online identifies new words, including low frequency new words, with high precision and high recall rates.
Silencing of CHD5 Gene by Promoter Methylation in Leukemia

Chromodomain helicase DNA binding protein 5 (CHD5) was previously proposed to function as a potent tumor suppressor by acting as a master regulator of a tumor-suppressive network. CHD5 is down-regulated in several cancers, including leukemia and is responsible for tumor generation and progression. However, the mechanism of CHD5 down-regulation in leukemia is largely unknown. In this study, quantitative reverse-transcriptase polymerase chain reaction and western blotting analyses revealed that CHD5 was down-regulated in human leukemia cell lines and samples. Luciferase reporter assays showed that most of the baseline regulatory activity was localized from 500 to 200 bp upstream of the transcription start site. Bisulfite DNA sequencing of the identified regulatory element revealed that the CHD5 promoter was hypermethylated in human leukemia cells and samples. Thus, CHD5 expression was inversely correlated with promoter DNA methylation in these samples. Treatment with DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (DAC) activates CHD5 expression in human leukemia cell lines. In vitro luciferase reporter assays demonstrated that methylation of the CHD5 promoter repressed its promoter activity. Furthermore, a chromatin immunoprecipitation assay combined with qualitative PCR identified activating protein 2 (AP2) as a potential transcription factor involved in CHD5 expression and indicated that treatment with DAC increases the recruitment of AP2 to the CHD5 promoter. In vitro transcription-factor activity studies showed that AP2 over-expression was able to activate CHD5 promoter activity. Our findings indicate that repression of CHD5 gene expression in human leukemia is mediated in part by DNA methylation of its promoter.
The use of positional information in the modeling of plants

We integrate into plant models three elements of plant representation identified as important by artists: posture (manifested in curved stems and elongated leaves), gradual variation of features, and the progression of the drawing process from overall silhouette to local details. The resulting algorithms increase the visual realism of plant models by offering an intuitive control over plant form and supporting an interactive modeling process. The algorithms are united by the concept of expressing local attributes of plant architecture as functions of their location along the stems.
High-value Applications of Nanocellulose

Nanocelluloses, obtained from the biopolymer cellulose, are a class of renewable functional nanomaterials with excellent properties and a broad range of applications. This review mainly illustrates practical and advanced applications of nanocellulose-based materials in the following categories. 1 Fire-resistant materials: in the section on these types of materials, the fireprotection property of nanocellulose/clay hybrid composites (clay nanopaper) is illustrated; oriented montmorillonite (MTM) provides barrier properties and low thermal conductivity whereas cellulose nanofibers (CNFs) impart favorable charring. 2 Thermal insulation materials: the best way to obtain materials with good heat insulation performance is to decrease the thermal conductivity of such materials. 3 Template materials: nanocellulose can direct the deposition and patterning of materials to form nanoparticles, nanowires, or nanotubes with improved properties. XiaoNan Hao, KaiWen Mou, XingYu Jiang, RuiTao Cha* 1. Beijing Engineering Research Center for BioNanotechnology and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China 2. University of Chinese Academy of Sciences, Beijing, 100049, China 3. School of Chemical Engineering and Material Science, Tianjin University of Science and Technology, Tianjin, 300457, China Received: 30 June 2017; accepted: 31 July 2017.
Hedera: Dynamic Flow Scheduling for Data Center Networks

Today's data centers offer tremendous aggregate bandwidth to clusters of tens of thousands of machines. However, because of limited port densities in even the highest-end switches, data center topologies typically consist of multi-rooted trees with many equal-cost paths between any given pair of hosts. Existing IP multipathing protocols usually rely on per-flow static hashing and can cause substantial bandwidth losses due to long-term collisions. In this paper, we present Hedera, a scalable, dynamic flow scheduling system that adaptively schedules a multi-stage switching fabric to efficiently utilize aggregate network resources. We describe our implementation using commodity switches and unmodified hosts, and show that for a simulated 8,192 host data center, Hedera delivers bisection bandwidth that is 96% of optimal and up to 113% better than static load-balancing methods.
Associations of family meal frequency with family meal habits and meal preparation characteristics among families of youth with type 1 diabetes.

BACKGROUND While benefits of family mealtimes, such as improved dietary quality and increased family communication, have been well-documented in the general population, less is known about family meal habits that contribute to more frequent family meals in youth with type 1 diabetes. METHODS This cross-sectional study surveyed 282 youth ages 8-18 years with type 1 diabetes and their parents on measures regarding diabetes-related and dietary behaviours. T-tests determined significant differences in youth's diet quality, adherence to diabetes management and glycaemic control between those with and without regular family meals (defined as ≥ 5 meals per week). Logistic regression analyses determined unadjusted and adjusted associations of age, socio-demographics, family meal habits, and family meal preparation characteristics with regular family meals. RESULTS 57% of parents reported having regular family meals. Families with regular family meals had significantly better diet quality as measured by the Healthy Eating Index (P < 0.05) and the NRF9.3 (P < 0.01), and adherence to diabetes management (P < 0.001); the difference in glycaemic control approached statistical significance (P = 0.06). Priority placed on, pleasant atmosphere and greater structure around family meals were each associated with regular family meals (P < 0.05). Meals prepared at home were positively associated with regular family meals, while convenience and fast foods were negatively associated (P < 0.05). Families in which at least one parent worked part-time or stayed at home were significantly more likely to have regular family meals than families in which both parents worked full-time (P < 0.05). In the multivariate logistic regression model, greater parental priority given to family mealtimes (P < 0.001) and more home-prepared meals (P < 0.001) predicted occurrence of regular family meals; adjusting for parent work status and other family meal habits. CONCLUSIONS Strategies for promoting families meals should not only highlight the benefits of family meals, but also facilitate parents' skills for and barriers to home-prepared meals.
VKORC1 Common Variation and Bone Mineral Density in the Third National Health and Nutrition Examination Survey

Osteoporosis, defined by low bone mineral density (BMD), is common among postmenopausal women. The distribution of BMD varies across populations and is shaped by both environmental and genetic factors. Because the candidate gene vitamin K epoxide reductase complex subunit 1 (VKORC1) generates vitamin K quinone, a cofactor for the gamma-carboxylation of bone-related proteins such as osteocalcin, we hypothesized that VKORC1 genetic variants may be associated with BMD and osteoporosis in the general population. To test this hypothesis, we genotyped six VKORC1 SNPs in 7,159 individuals from the Third National Health and Nutrition Examination Survey (NHANES III). NHANES III is a nationally representative sample linked to health and lifestyle variables including BMD, which was measured using dual energy x-ray absorptiometry (DEXA) on four regions of the proximal femur. In adjusted models stratified by race/ethnicity and sex, SNPs rs9923231 and rs9934438 were associated with increased BMD (p = 0.039 and 0.024, respectively) while rs8050894 was associated with decreased BMD (p = 0.016) among non-Hispanic black males (n = 619). VKORC1 rs2884737 was associated with decreased BMD among Mexican-American males (n = 795; p = 0.004). We then tested for associations between VKORC1 SNPs and osteoporosis, but the results did not mirror the associations observed between VKORC1 and BMD, possibly due to small numbers of cases. This is the first report of VKORC1 common genetic variation associated with BMD, and one of the few reports available that investigate the genetics of BMD and osteoporosis in diverse populations.
Sense in expressive music performance: Data acquisition, computational studies, and models

This chapter gives an introduction into basic strands of current research in expressive music performance. A special focus is given on the various methods to acquire performance data either during a performance (e.g., through computer-monitored instruments) or from audio recordings. We then overview the different computational approaches to formalise and model the various aspects in expressive music performance. Future challenges and open problems are tackled briefly at the end of this chapter.
Quantitative EEG markers in severe post-resuscitation brain injury with therapeutic hypothermia

Therapeutic hypothermia has been regarded as one of the most effective post-cardiac arrest (CA) treatments to improve survival and functional recovery. However, many clinical prognostic markers after resuscitation have become less reliable under hypothermia. In this study, we applied and compared two developed quantitative measures - information quantity (IQ) and sub-band IQ (SIQ) - to evaluate the accuracy of EEG markers on predicting cortical recovery under therapeutic hypothermia. A total of 14 rats under 9-min asphyxial-CA, leading to severe brain injury, were randomly divided into two groups: hypothermia (32°C-34°C) and normothermia (36.5-37.5°C) (n=7 per group). For each rat, EEG and temperature were continuously recorded for the first 15 hrs. EEG was then recorded for serial 30 mins at 24, 48 and 72 hrs. The neurologic deficit score was evaluated daily to assess the neurologic recovery. Early SIQ and IQ were both significantly correlated with the 72-hr NDS, when the rats remained comatose. Both IQ and SIQ were able to discriminate the animals with good and bad functional outcomes starting from 1 hr after resuscitation. There was no significant difference in 72-hr NDS results (hypothermia (median (25th, 75th), 65 (52, 67)) versus normothermia (53.5 (52.25, 66.75))) (p>0.05) due to the high mortality rate (5/14) with severe brain injury. Contrary to IQ recovery but similarly to NDS scores, the SIQ recovery was not significantly different between the hypothermia (0.66±0.04) and normothermia (0.64±0.04) groups (p>0.05). IQ could identify the presence of high-frequency oscillations during the recovery from severe brain injury. We demonstrated that while SIQ was able to provide additional sub-band EEG information related to the recovery of different brain functions, both early IQ and SIQ markers are able to accurately predict neurologic outcome after CA.
Total Convexity for Powers of the Norm in Uniformly Convex Banach Spaces

We show that in any uniformly convex Banach space the functions f(x) = kxk r with r 2 (1;1) are totally convex. Using this fact we establish a formula for determining Bregman projections on closed hyperplanes and half spaces. This leads to a method for solving linear operator equations (e.g., flrst kind Fredholm and Volterra equations) in spaces which are uniformly convex and smooth.
Idiopathic retroperitoneal fibrosis: a rare onset of the illness caused by haemorrhagic fever with renal syndrome.

Sir, Idiopathic retroperitoneal fibrosis (IRF) is a collagen vascular disease of unknown aetiology. It is characterized by chronic, non-specific retroperitoneal inflammation, which may cause ureteric obstruction. Many authors believe that it is a type of immune disorder [1]. Bosnia and Herzegovina is known as a region where Hanta virus infection has been endemic for >50 years [2]. A case of IRF associated with haemorrhagic fever with renal syndrome (HFRS) has not been reported up to now. A 44-year-old, previously healthy man was hospitalized with acute renal failure. He was febrile 2 days before admission, had dull abdominal pain, decreased urine output, shortness of breath, diarrhoea and arterial hypertension (190/120mmHg). Blood tests showed metabolic acidosis (HCO3: 15.9mmol/l) and increased C-reactive protein (11.26mg/l), potassium (7.9mmol/l), serum creatinine (884 mmol/l), blood urea nitrogen (17.6mmol/l) and globulins (49.1 g/l) and decreased haemoglobin (7.4mmol/l). Urinanalysis showed proteinuria and leukocyturia. Urine culture was negative. Indirect immunofluorescene tests for Hanta viruses were positive for Pummala virus. Ultrasound showed acute renal parenchymal lesions with bilateral hydronephrosis, grades I–II, and widening of the wall of the abdominal aorta. The presence of a great number of rodents in the forest where the patient was working has been reported by the epidemiology service. After supportive, antihypertensive and diuretic therapy, the patient’s renal function stabilized, with serum creatinine at 187 mmol/l and potassium at 4.5mmol/l. Intravenous urography showed a functioning left kidney, with a suspected retrocaval ureter on the right side and dilation of the channels of the right kidney. A computed tomography contrast scan showed a solid retroperitoneal mass, in the form of thick plate of high density, extending from the level of the renal hilum down caudally to the bifurcation of the aorta (compatible with retroperitoneal fibrosis). A double-J stent was applied and steroids and androgens were administered (pronison 60mg plus tamoxifen 20mg 2). After 3 months, the stents were removed and medications were continued. After 6 months, the patient’s total DTPA clearance was 61.1ml/min (11.8ml/min in the left kidney and 49.3ml/min in the right kidney), measured by technetium marked by diethylaminoacid. Steroids and androgens were withdrawn after 12 months. The patient has normal blood pressure and stable renal function, with serum creatinine at 125mmol/l. It remains a mystery whether HFRS triggered an immune abnormality and acceleration of the symptoms of a latent IRF or whether the two diseases merely coincided. Adequate treatment of HFRS was certainly the reason that renal function recovered and the progression of the disorder caused by the chronic disease, IRF, was hampered.