Natural Language to Code Translation with Execution

Generative models of code, pretrained on large corpora of programs, have shown great success in translating natural language to code (Chen et al., 2021; Austin et al., 2021; Li et al., 2022, inter alia). While these models do not explicitly incorporate program semantics (i.e., execution results) during training, they are able to generate correct solutions for many problems. However, choosing a single correct program from a generated set for each problem remains challenging. In this work, we introduce execution result--based minimum Bayes risk decoding (MBR-EXEC) for program selection and show that it improves the few-shot performance of pretrained code models on natural-language-to-code tasks. We select output programs from a generated candidate set by marginalizing over program implementations that share the same semantics. Because exact equivalence is intractable, we execute each program on a small number of test inputs to approximate semantic equivalence. Across datasets, execution or simulated execution significantly outperforms the methods that do not involve program semantics. We find that MBR-EXEC consistently improves over all execution-unaware selection methods, suggesting it as an effective approach for natural language to code translation. We open-source our code at github.com/facebookresearch/mbr-exec and data at dl.fbaipublicfiles.com/mbr-exec/mbr-exec-release.zipComment: EMNLP 202

Local-scale forcing effects on wind flows in an urban environment: Impact of geometrical simplifications

Wind flow in urban areas is strongly affected by the urban geometry. In the last decades most of the geometries used to reproduce urban areas, both in wind-tunnel (WT) tests and Computational Fluid Dynamics (CFD) simulations, were simplified compared to reality in order to limit experimental effort and computational costs. However, it is unclear to which extent these geometrical simplifications can affect the reliability of the numerical and experimental results. The goal of this paper is to quantify the deviations caused by geometrical simplifications. The case under study is the district of Livorno city (Italy), called \ue2\u80\u9cQuartiere La Venezia\ue2\u80\u9d. The 3D steady Reynolds-averaged Navier-Stokes (RANS) simulations are solved, first for a single block of the district, then for the whole district. The CFD simulations are validated with WT tests at scale 1:300. Comparisons are made of mean wind velocity profiles between WT tests and CFD simulations, and the agreement is quantified using four validation metrics (FB, NMSE, R and FAC1.3). The results show that the most detailed geometry provides improved performance, especially for wind direction \uce\ub1 = 240\uc2\ub0 (22% difference in terms of FAC1.3)

Biofuel as Alternative Energy Carrier : Current Status, European Policies, Market and Production Level

Biofuels could be an appropriate way to reduce green house gas (GHG) emissions and to reduce the amount of fossil fuels burned. Two most common types of biofuels which are being developed and presently available on a commercial basis, are Ethanol and Biodiesel along with their derivatives. Biodiesel is the biofuel with the most rapid rate of market growth. European biodiesel industry is well established with a significant continuous increase in its production. In order to support the use of biodiesel and biofuel World-wide, especially, in developing countries where fossil energy use GHG emission will rise exponentially, there is a utmost necessity for international co-operation. The questions of biofuel industrial production, financial incentives, legislation, investment potential et. al. will be discussed in this publication.Використання біопалива може істотно знизити емісію парникових газів та скоротити кількість викопного палива, що спалюється. Найбільш поширеними та такими, що знайшли комерційне застосування, видами біопалива є біоетанол та біодизель з їх похідними. Застосування біодизеля характеризується найбільш активно зростаючим ринковим попитом, а Європейська біодизельна індустрія є стабільною з суттєвим постійним зростанням виробництва. Для забезпечення широкомасштабного, на світовому рівні, застосування біопалив, особливо в країнах, що розвиваються, де емісія парникових газів внаслідок використання викопних палив експоненційно зростає, вкрай необхідним є міжнародне співробітництво. У статті обговорюються питання промислового виробництва біопалива, фінансового стимулювання, законодавчої діяльності, інвестиційного потенціалу та ін.Использование биотоплива может существенно снизить эмиссию парниковых газов и сократить количество сжигаемых ископаемых топлив. Наиболее распространенными и нашедшими коммерческое применение видами биотоплива являются биоэтанол и биодизель наряду с их производными. Применение биодизеля характеризуется наиболее активно растущим рыночным спросом, а Европейская биодизельная индустрия является стабильной с существенным постоянным ростом производства. Для обеспечения широкомасштабного, на мировом уровне, применения биотоплив, особенно в развивающихся странах, где эмиссия парниковых газов вследствие использования ископаемых топлив экспоненциально возрастает, крайне необходимым является международное сотрудничество. В статье обсуждаются вопросы промышленного производства биотоплива, финансового стимулирования, законодательной деятельности, инвестиционного потенциала и др

Psychology and hereditary angioedema: A systematic review

Background: Hereditary angioedema (HAE) is caused by mutations in the C1 inhibitor (C1-INH) gene Serpin Family G Member 1(SERPING1), which results in either the decreased synthesis of normal C1-INH (C1-INH–HAE type I) or expression of unfunctional C1-INH (C1-INH–HAE type II). In recent studies, emotional stress was reported by patients as the most common trigger factor for C1-INH–HAE attacks. Moreover, patients reported considerable distress over the significant variability and uncertainty with which the disease manifests, in addition to the impact of physical symptoms on their overall quality of life. Objective: We did a systematic review of the literature to shed light on the advancements made in the study of how stress and psychological processes impact C1-INH–HAE. Methods: All of the articles on C1-INH–HAE were analyzed up to December 2019. Both medical data bases and psychological data bases were examined. The keywords (KWs) used for searching the medical and psychological data bases were the following: “hereditary angioedema,” “psychology,” “stress,” “anxiety,” and “depression.” Results: Of a total of 2549 articles on C1-INH–HAE, 113 articles were retrieved from the literature search by using the related KWs. Twenty-one of these articles were retrieved, examined, and classified. Conclusion: Although the literature confirmed that stress may induce various physical diseases, it also warned against making simplistic statements about its incidence that did not take into account the complexity and multicausality of factors that contribute to C1-INH–HAE expression

Transcriptome sequencing study implicates immune-related genes differentially expressed in schizophrenia: new data and a meta-analysis

We undertook an RNA sequencing (RNAseq)-based transcriptomic profiling study on lymphoblastoid cell lines of a European ancestry sample of 529 schizophrenia cases and 660 controls, and found 1058 genes to be differentially expressed by affection status. These differentially expressed genes were enriched for involvement in immunity, especially the 697 genes with higher expression in cases. Comparing the current RNAseq transcriptomic profiling to our previous findings in an array-based study of 268 schizophrenia cases and 446 controls showed a highly significant positive correlation over all genes. Fifteen (18%) of the 84 genes with significant (false discovery rateo0.05) expression differences between cases and controls in the previous study and analyzed here again were differentially expressed by affection status here at a genome-wide significance level (Bonferroni Po0.05 adjusted for 8141 analyzed genes in total, or Po ~ 6.1 × 10− 6), all with the same direction of effect, thus providing corroborative evidence despite each sample of fully independent subjects being studied by different technological approaches. Meta-analysis of the RNAseq and array data sets (797 cases and 1106 controls) showed 169 additional genes (besides those found in the primary RNAseq-based analysis) to be differentially expressed, and provided further evidence of immune gene enrichment. In addition to strengthening our previous array-based gene expression differences in schizophrenia cases versus controls and providing transcriptomic support for some genes implicated by other approaches for schizophrenia, our study detected new genes differentially expressed in schizophrenia. We highlight RNAseq-based differential expression of various genes involved in neurodevelopment and/or neuronal function, and discuss caveats of the approach

Transcriptomic signatures of schizophrenia revealed by dopamine perturbation in an ex vivo model

The dopaminergic hypothesis of schizophrenia (SZ) postulates that dopaminergic over activity causes psychosis, a central feature of SZ, based on the observation that blocking dopamine (DA) improves psychotic symptoms. DA is known to have both receptor- and non-receptor-mediated effects, including oxidative mechanisms that lead to apoptosis. The role of DA-mediated oxidative processes in SZ has been little studied. Here, we have used a cell perturbation approach and measured transcriptomic profiles by RNAseq to study the effect of DA exposure on transcription in B-cell transformed lymphoblastoid cell lines (LCLs) from 514 SZ cases and 690 controls. We found that DA had widespread effects on both cell growth and gene expression in LCLs. Overall, 1455 genes showed statistically significant differential DA response in SZ cases and controls. This set of differentially expressed genes is enriched for brain expression and for functions related to immune processes and apoptosis, suggesting that DA may play a role in SZ pathogenesis through modulating those systems. Moreover, we observed a non-significant enrichment of genes near genome-wide significant SZ loci and with genes spanned by SZ-associated copy number variants (CNVs), which suggests convergent pathogenic mechanisms detected by both genetic association and gene expression. The study suggests a novel role of DA in the biological processes of immune and apoptosis that may be relevant to SZ pathogenesis. Furthermore, our results show the utility of pathophysiologically relevant perturbation experiments to investigate the biology of complex mental disorders

Metformin Activates an Atypical PKC-CBP Pathway to Promote Neurogenesis and Enhance Spatial Memory Formation

SummaryAlthough endogenous recruitment of adult neural stem cells has been proposed as a therapeutic strategy, clinical approaches for achieving this are lacking. Here, we show that metformin, a widely used drug, promotes neurogenesis and enhances spatial memory formation. Specifically, we show that an atypical PKC-CBP pathway is essential for the normal genesis of neurons from neural precursors and that metformin activates this pathway to promote rodent and human neurogenesis in culture. Metformin also enhances neurogenesis in the adult mouse brain in a CBP-dependent fashion, and in so doing enhances spatial reversal learning in the water maze. Thus, metformin, by activating an aPKC-CBP pathway, recruits neural stem cells and enhances neural function, thereby providing a candidate pharmacological approach for nervous system therapy.Video Abstrac

The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

Peer reviewedPublisher PD

Cancer survivors' experience with telehealth: A systematic review and thematic synthesis

Background: Net survival rates of cancer are increasing worldwide, placing a strain on health service provision. There is a drive to transfer the care of cancer survivors—individuals living with and beyond cancer—to the community and encourage them to play an active role in their own care. Telehealth, the use of technology in remote exchange of data and communication between patients and health care professionals (HCPs), is an important contributor to this evolving model of care. Telehealth interventions are “complex,” and understanding patient experiences of them is important in evaluating their impact. However, a wider view of patient experience is lacking as qualitative studies detailing cancer survivor engagement with telehealth are yet to be synthesized. Objective: To systematically identify, appraise, and synthesize qualitative research evidence on the experiences of adult cancer survivors participating in telehealth interventions, to characterize the patient experience of telehealth interventions for this group. Methods: Medline (PubMed), PsychINFO, Cumulative Index for Nursing and Allied Health Professionals (CINAHL), Embase, and Cochrane Central Register of Controlled Trials were searched on August 14, 2015, and March 8, 2016, for English-language papers published between 2006 and 2016. Inclusion criteria were as follows: adult cancer survivors aged 18 years and over, cancer diagnosis, experience of participating in a telehealth intervention (defined as remote communication or remote monitoring with an HCP delivered by telephone, Internet, or hand-held or mobile technology), and reporting qualitative data including verbatim quotes. An adapted Critical Appraisal Skill Programme (CASP) checklist for qualitative research was used to assess paper quality. The results section of each included article was coded line by line, and all papers underwent inductive analysis, involving comparison, reexamination, and grouping of codes to develop descriptive themes. Analytical themes were developed through an iterative process of reflection on, and interpretation of, the descriptive themes within and across studies. Results: Across the 22 included papers, 3 analytical themes emerged, each with 3 descriptive subthemes: (1) influence of telehealth on the disrupted lives of cancer survivors (convenience, independence, and burden); (2) personalized care across physical distance (time, space, and the human factor); and (3) remote reassurance—a safety net of health care professional connection (active connection, passive connection, and slipping through the net). Telehealth interventions represent a convenient approach, which can potentially minimize treatment burden and disruption to cancer survivors’ lives. Telehealth interventions can facilitate an experience of personalized care and reassurance for those living with and beyond cancer; however, it is important to consider individual factors when tailoring interventions to ensure engagement promotes benefit rather than burden. Conclusions: Telehealth interventions can provide cancer survivors with independence and reassurance. Future telehealth interventions need to be developed iteratively in collaboration with a broad range of cancer survivors to maximize engagement and benefit

SHP-1 negatively regulates neuronal survival by functioning as a TrkA phosphatase

Nerve growth factor (NGF) mediates the survival and differentiation of neurons by stimulating the tyrosine kinase activity of the TrkA/NGF receptor. Here, we identify SHP-1 as a phosphotyrosine phosphatase that negatively regulates TrkA. SHP-1 formed complexes with TrkA at Y490, and dephosphorylated it at Y674/675. Expression of SHP-1 in sympathetic neurons induced apoptosis and TrkA dephosphorylation. Conversely, inhibition of endogenous SHP-1 with a dominant-inhibitory mutant stimulated basal tyrosine phosphorylation of TrkA, thereby promoting NGF-independent survival and causing sustained and elevated TrkA activation in the presence of NGF. Mice lacking SHP-1 had increased numbers of sympathetic neurons during the period of naturally occurring neuronal cell death, and when cultured, these neurons survived better than wild-type neurons in the absence of NGF. These data indicate that SHP-1 can function as a TrkA phosphatase, controlling both the basal and NGF-regulated level of TrkA activity in neurons, and suggest that SHP-1 regulates neuron number during the developmental cell death period by directly regulating TrkA activity