Miracle-dz/UniFAR-FTUs huggingface dataset:
TreeFuser: a framework for analyzing and fusing general recursive tree traversals

Series of traversals of tree structures arise in numerous contexts: abstract syntax tree traversals in compiler passes, rendering traversals of the DOM in web browsers, kd-tree traversals in computational simulation codes. In each of these settings, a tree is traversed multiple times to compute various values and modify various portions of the tree. While it is relatively easy to write these traversals as separate small updates to the tree, for efficiency reasons, traversals are often manually fused to reduce the number of times that each portion of the tree is traversed: by performing multiple operations on the tree simultaneously, each node of the tree can be visited fewer times, increasing opportunities for optimization and decreasing cache pressure and other overheads. This fusion process is often done manually, requiring careful understanding of how each of traversals of the tree interact. This paper presents an automatic approach to traversal fusion: tree traversals can be written independently, and then our framework analyzes the dependences between the traversals to determine how they can be fused to reduce the number of visits to each node in the tree. A critical aspect of our framework is that it exploits two opportunities to increase the amount of fusion: i) it automatically integrates code motion, and ii) it supports partial fusion, where portions of one traversal can be fused with another, allowing for a reduction in node visits without requiring that two traversals be fully fused. We implement our framework in Clang, and show across several case studies that we can successfully fuse complex tree traversals, reducing the overall number of traversals and substantially improving locality and performance.
Genome-Wide Analysis of the bZIP Gene Family Identifies Two ABI5-Like bZIP Transcription Factors, BrABI5a and BrABI5b, as Positive Modulators of ABA Signalling in Chinese Cabbage

bZIP (basic leucine zipper) transcription factors coordinate plant growth and development and control responses to environmental stimuli. The genome of Chinese cabbage (Brassica rapa) encodes 136 putative bZIP transcription factors. The bZIP transcription factors in Brassica rapa (BrbZIP) are classified into 10 subfamilies. Phylogenetic relationship analysis reveals that subfamily A consists of 23 BrbZIPs. Two BrbZIPs within subfamily A, Bra005287 and Bra017251, display high similarity to ABI5 (ABA Insensitive 5). Expression of subfamily A BrbZIPs, like BrABI5a (Bra005287/BrbZIP14) and BrABI5b (Bra017251/BrbZIP13), are significantly induced by the plant hormone ABA. Subcellular localization assay reveal that both BrABI5a and BrABI5b have a nuclear localization. BrABI5a and BrABI5b could directly stimulate ABA Responsive Element-driven HIS (a HIS3 reporter gene, which confers His prototrophy) or LUC (LUCIFERASE) expression in yeast and Arabidopsis protoplast. Deletion of the bZIP motif abolished BrABI5a and BrABI5b transcriptional activity. The ABA insensitive phenotype of Arabidopsis abi5-1 is completely suppressed in transgenic lines expressing BrABI5a or BrABI5b. Overall, these results suggest that ABI5 orthologs, BrABI5a and BrABI5b, have key roles in ABA signalling in Chinese cabbage.
Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq

Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids.
Comprehensive Analysis of Long Non-Coding RNAs in Ovarian Cancer Reveals Global Patterns and Targeted DNA Amplification

Long non-coding RNAs (lncRNAs) are emerging as potent regulators of cell physiology, and recent studies highlight their role in tumor development. However, while established protein-coding oncogenes and tumor suppressors often display striking patterns of focal DNA copy-number alteration in tumors, similar evidence is largely lacking for lncRNAs. Here, we report on a genomic analysis of GENCODE lncRNAs in high-grade serous ovarian adenocarcinoma, based on The Cancer Genome Atlas (TCGA) molecular profiles. Using genomic copy-number data and deep coverage transcriptome sequencing, we derived dual copy-number and expression data for 10,419 lncRNAs across 407 primary tumors. We describe global correlations between lncRNA copy-number and expression, and associate established expression subtypes with distinct lncRNA signatures. By examining regions of focal copy-number change that lack protein-coding targets, we identified an intergenic lncRNA on chromosome 1, OVAL, that shows narrow focal genomic amplification in a subset of tumors. While weakly expressed in most tumors, focal amplification coincided with strong OVAL transcriptional activation. Screening of 16 other cancer types revealed similar patterns in serous endometrial carcinomas. This shows that intergenic lncRNAs can be specifically targeted by somatic copy-number amplification, suggestive of functional involvement in tumor initiation or progression. Our analysis provides testable hypotheses and paves the way for further study of lncRNAs based on TCGA and other large-scale cancer genomics datasets.
Unsafe sleep practices and an analysis of bedsharing among infants dying suddenly and unexpectedly: results of a four-year, population-based, death-scene investigation study of sudden infant death syndrome and related deaths.

BACKGROUND Prone sleep and unsafe sleep surfaces increase the risk of sudden infant death. Recent epidemiologic studies also suggest that when an infant's head or face is covered by bedding, or when a sleep surface is shared with others, the risk of dying increases. The inference of a causal role for these risk factors is supported by physiologic studies and by the consistent finding that fewer infants die when risk factors are reduced. The prevalence of most of these risk factors in infant deaths in the United States is uncertain. OBJECTIVE To describe the prevalence of several important risk factors related to sleep practices among a defined population of infants dying suddenly and unexpectedly. METHODS In this population-based study, we retrospectively reviewed death-scene information and medical examiners' investigations of deaths in the city of St Louis and St Louis County between January 1, 1994 and December 31, 1997. Because of the potential for diagnostic overlap, all deaths involving infants <2 years old with the diagnoses of sudden infant death syndrome (SIDS), accidental suffocation, or cause undetermined were included. RESULTS The deaths of 119 infants were studied. Their mean age was 109.3 days (range: 6-350). The diagnoses were SIDS in 88 deaths, accidental suffocation in 16, and undetermined in 15. Infants were found prone in 61.1% of cases and were found on a sleep surface not designed for infants in 75.9%. The head or face was covered by bedding in 29.4%. A shared sleep surface was the site of death in 47.1%. Only 8.4% of deaths involved infants found nonprone and alone, with head and face uncovered. CONCLUSIONS Using detailed death-scene descriptions, we found that similar unsafe sleeping practices occurred in the large majority of cases diagnosed as SIDS, accidental suffocation, and cause undetermined. Considering these diagnoses together may be useful in public health campaigns during a time when there may be diagnostic overlap. Regardless of the diagnosis, recommendations that infants sleep supine on firm sleep surfaces that lessen the risk of entrapment or head covering have the potential to save many lives. Campaigns are needed to heighten awareness of these messages and of the risks of dangerous bedsharing.
Australian psychologists' perceptions and experiences of client threats

There is empirical evidence that workplace violence is increasing, particularly in settings where health care professionals such as psychologists are employed, and often these incidents are perpetrated by clients. Given that client violence can have wide ranging and serious consequences, it is not surprising that researchers are focussing on this issue. One notable finding is that psychologists feel that they do not have the training or confidence to manage the violent behaviour of clients. A review of the relevant literature was undertaken to determine why psychologists feel ill prepared for such incidents. Whilst there is a wide range of definitions of client violence, it appears that many of the professionals’ concerns about various forms of client behaviour go beyond these definitions of violence. There is an array of client behaviours that make professionals feel their wellbeing is at risk which fall outside the general definition of violence. Consequently, the term client threats may be more appropriate. There is no research in which psychologists were directly asked what client interactions they perceived as putting their wellbeing at risk and, without this information, professional advice to them may not be effective. The purpose of this research project was to determine psychologists’ experiences and perceptions of client threats. Stage 1 included interviews with 45 psychologists which indicated that their experiences and perceptions of client threats could be best conceptualised by developing a preliminary theory of client threat. In stage 2 a Delphi approach, with a panel of experts, helped formulate a modified Client Threat Theory that proposes a three phase model outlining the process through which psychologists experience these threats. This theory begins with a client behaviour being observed and conceptualised as a threat (activation phase), then influential factors are assessed (risk assessment), and lastly a management plan is formulated and applied in response to the threat (execution phase). This research project also provides a detailed understanding of how the participating psychologists experienced client threats. It was discovered that threatening experiences were triggered by more than violent client behaviours and that a term broader than violence was needed to encompass these experiences. The types of threats reportedly experienced by participants were physical, sexual, verbal, Psychologists’ Client Threat Experiences ii psychological, reputational, and financial in nature. Participants also reported feeling threatened when they perceived that a client behaved in a threatening manner towards people known to them, such as colleagues and family members. This provides a basis from which future researchers could develop a comprehensive definition and theory of client threat, along with efficient and effective tools to reduce its occurrence and deal with it more effectively. Psychologists’ Client Threat Experiences iii
Fertilization envelope assembly in sea urchin eggs inseminated in chloride‐deficient sea water: II. Biochemical effects

Eggs of the sea urchin Strongylocentrotus purpuratus were fertilized in normal and in several chloride‐deficient sea waters ([CI−]: normal > isethionate > methyl sulfonate > bromide). The fertilization envelopes (FE) were thinner and failed to harden, and the characteristic I‐T transition did not occur. The permeability of the experimental FEs, as determined by release of protein from the perivitelline space, increased in the order of decreasing [CI−]. Release of the enzymes β‐1, 3‐glucanase and cortical granule protease were not significantly altered. On the other hand, release of ovoperoxidase was increased three to four times in bromide sea water. Furthermore, a dose‐response was observed in varying concentrations of bromide‐normal sea water. With decreasing chloride (increasing bromide) concentration, more ovoperoxidase activity was observed. Cytochemical localization of ovoperoxidase activity with diaminobenzidine revealed almost a total lack of staining of FEs from bromide‐substituted sea water. The results suggest that in chloride‐deficient sea waters protein incorporation into the nascent FE is impaired. At least in the case of bromide, the incorporation of ovoperoxidase into the nascent FE was also inhibited.
Molecular cloning and characterization of a midgut chymotrypsin-like enzyme from the lesser grain borer, Rhyzopertha dominica.

A cDNA encoding a chymotrypsinogen-like protein in midguts of the lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae) was cloned and sequenced. The 901 bp cDNA contains an 816-nucleotide open reading frame encoding 272-amino acids. The predicted molecular mass and pI of the mature enzyme are 23.7 kDa and 4.64, respectively. The encoded protein includes amino acid sequence motifs that are conserved with 5 homologous chymotrypsinogen proteins from other insects. Features of the putative chymotrypsin-like protein from R. dominica include the serine proteinase active site (His(90), Asp(133), Ser(226)), conserved cysteine residues for disulfide bridges, the residues (Gly(220), Gly(243), Asp(252)) that determine chymotrypsin specificity, and both zymogen activation and signal peptides. A TPCK-sensitive caseinolytic protein (P6) with an estimated molecular mass of 24 kDa is present in midgut extracts of R. dominica and can be resolved by electrophoresis on 4-16% polyacrylamide gels. The molecular mass of this caseinolytic enzyme is similar to that of the chymotrypsin deduced from cDNA. Midgut extracts of R. dominica readily hydrolyzed azocasein and N-succinyl-alanine-alanine-proline-phenylalanine-p- nitroanilide (SAAPFpNA), a chymotrypsin-specific substrate. Properties of the enzymes responsible for these activities were partially characterized with respect to distribution in the gut, optimum pH, and sensitivity toward selected proteinase inhibitors. Optimal activity against both azocasein and SAAPFpNA occurs in a broad pH range from about 7 to 10. Both azocasein and SAAPFpNA activities, located primarily in the anterior midgut region, are inhibited by aprotinin, phenylmethyl sulphonylfluoride (PMSF), and soybean trypsin inhibitor (STI). TPCK (N-alpha-tosyl-L-phenylalanine chloromethyl ketone) and chymostatin inhibited more than 60% of SAAPFpNA but only about 10-20% of azocasein activity. These results provide additional evidence for the presence of serine proteinases, including chymotrypsin, in midguts of R. dominica. Arch. Insect Biochem. Physiol. 43:173-184, 2000.Published 2000 Wiley-Liss, Inc.
Prenatal sonographic findings in a case of Wolman's disease

No published case of Wolman's disease has described the prenatal sonographic findings. We present a case in which a third‐trimester sonographic examination demonstrated fetal hepatomegaly and bilateral adrenal echogenicity suggestive of diffuse calcification. Wolman's disease, also known as lysosomal acid lipase (LIPA) deficiency, is a rare autosomal‐recessive disorder characterized by complete absence of the LIPA enzyme. The diagnosis of Wolman's disease was made postnatally by biochemical testing, which indicated absence of LIPA enzyme activity and gene sequencing, which confirmed homozygosity for the G66V mutation within the LIPA gene. © 2017 Wiley Periodicals, Inc. J Clin Ultrasound 46:66–68, 2018;
Social Support as a Moderator Between Victimization and Internalizing–Externalizing Distress From Bullying

Although it is important to study the negative outcomes experienced by victims of bullying, it is equally important to study the factors that may buffer victims from distress. Thus, the relationship among social support, victimization, and internalizing-externalizing distress from bullying was investigated. Participants were 355 middle school students who completed the Child and Adolescent Social Support Scale (Malecki, Demaray, & Elliott, 2000) and scales from the Reynolds Bully-Victimization Scales for Schools (Reynolds, 2003). Teacher, classmate, and school support for males and parent support for females moderated the relationship between victimization and internalizing distress from bullying. Close friend support for females moderated the relationship between victimization and externalizing distress from bullying, however, in a direction opposite to that predicted. Results indicate that social support may play a buffering role between victimization and internalizing distress from bullying.
Regulatory Role of Autophagy in Globular Adiponectin-Induced Apoptosis in Cancer Cells

Adiponectin, an adipokine predominantly secreted from adipose tissue, exhibits diverse biological responses, including metabolism of glucose and lipid, and apoptosis in cancer cells. Recently, adiponectin has been shown to modulate autophagy as well. While emerging evidence has demonstrated that autophagy plays a role in the modulation of proliferation and apoptosis of cancer cells, the role of autophagy in apoptosis of cancer cell caused by adiponectin has not been explored. In the present study, we demonstrated that globular adiponectin (gAcrp) induces both apoptosis and autophagy in human hepatoma cell line (HepG2 cells) and breast cancer cells (MCF-7), as evidenced by increase in caspase-3 activity, Bax, microtubule-associated protein light chain 3-II (LC3 II) protein levels, and autophagosome formation. Interestingly, gene silencing of LC3B, an autophagy marker, significantly enhanced gAcrp-induced apoptosis in both HepG2 and MCF-7 cell lines, whereas induction of autophagy by rapamycin, an mTOR inhibitor, significantly prevented gAcrp-induced apoptosis in hepatoma cells HepG2. Furthermore, modulation of autophagy produced similar effects on gAcrp-induced Bax expression in HepG2 cells. These results implicate that induction of autophagy plays a regulatory role in adiponectin-induced apoptosis of cancer cells, and thus inhibition of autophagy would be a novel promising target to enhance the efficiency of cancer cell apoptosis by adiponectin.
Biomass smoke COPD has less tomographic abnormalities but worse hypoxemia compared with tobacco COPD

Special attention has emerged towards biomass smoke-induced chronic obstructive pulmonary disease (COPD), providing new knowledge for prevention and therapeutic approach of non-smoker COPD patients. However, the understanding of biomass smoke COPD is still limited and somewhat controversial. The aim of the present study was to compare COPD exclusively caused by tobacco smoking with COPD exclusively caused by environmental or occupational exposures. For this cross-sectional study, COPD patients were recruited from outpatient clinics and formed two groups: non-smoker COPD group (n=16) with exposure to biomass smoke who did not smoke cigarette and tobacco smoker COPD group (n=15) with people who did not report biomass smoke exposure. Subjects underwent pulmonary function tests, thoracic high-resolution computed tomography, 6-min walk test, and sputum induction. The non-smoker COPD group had biomass smoke exposure of 133.3±86 hour-years. The tobacco COPD group smoked 48.5±27.4 pack-years. Women were 62.5 and 66.7%, respectively, of non-smokers and smokers. The non-smoker COPD group showed higher prevalence of dyspnea, lower arterial oxygen tension (PaO2), and lower arterial oxygen saturation (SaO2%) with similar spirometry results, lung volumes, and diffusion capacity. Regarding inflammatory biomarkers, differences were detected in sputum number of lymphomononuclear cells and in sputum concentrations of interleukin (IL)-6 and IL-8 with higher values in the smoker group. Emphysema was more prevalent in the tobacco smoker group, which also showed higher relative bronchial wall thickness and lower lung density by quantitative analysis. Biomass smoke induced more hypoxemia compared to tobacco in COPD patients with similar severity.
Re-administration after the failure of gefitinib or erlotinib in patients with advanced non-small cell lung cancer.

OBJECTIVE Few treatment options are available for advanced non-small cell lung cancer (NSCLC) patients who have failed of gefitinib or erlotinib treatment in second/third-line treatment. The aim of this study was to investigate the efficacy of re-administration of the same TKI after failure of gefitinib or erlotinib. PATIENTS AND METHODS The clinical data of 33 patients with advanced NSCLC were retrospectively analyzed. All of the patients were given the same TKI treatment after the failure of gefitinib or erlotinib. Survival analysis was evaluated by Kaplan-Meier method. RESULTS Twenty patients (60.6%) were re-administration with gefitinib as the 2(nd) EGFR-TKI, and thirteen patients (39.4%) received erlotinib. One patient (3.0%) showed partial response (PR), 14 (42.4%) achieved stable disease (SD), and 18 (54.5%) had progressive disease (PD). The disease control rate was 45.5% and the median progression-free survival was 1.5 months (95% CI: 0.6-2.3 months). The PFS in patients who got disease control in the prior TKI was 2.2 and 1.2 months in the progression disease cases (P=0.29), the DCR was 54.5% and 27.3% in two group, respectively (P=0.26). CONCLUSIONS Re-administration of TKI seems to be a potential therapeutic option for treatment of selected advanced NSCLC patients after failure of geﬁtinib or erlotinib, especially for the patients with NSCLC who once responded from the prior TKI treatment.
Efficient Implementation of AES IP

The AES IP with different architectures implemented using ASIC and FPGA are presented in this paper. For ASIC design, the performance of the AES IP has been evaluated by comparing its area/power/delay, synthesized with TSMC 0.35 mum cell library and TSMC 0.18 mum cell library. The performance estimation in FPGA implementation with Altera and Xilinx platforms are also presented. The hardware implementation results of the proposed architecture with Mixcolumn/preprocess InvMixcolumn to perform Mixcolumn/InvMixcolumn transformation has less area cost as compared with previous relevant architecture. Due to the I/O bottlenecks between host processor and a stand alone AES module, a reconfigurable bandwidth sharing architecture is proposed to enhance the system performance