Deep Just-In-Time Inconsistency Detection Between Comments and Source Code

Natural language comments convey key aspects of source code such as implementation, usage, and pre- and post-conditions. Failure to update comments accordingly when the corresponding code is modified introduces inconsistencies, which is known to lead to confusion and software bugs. In this paper, we aim to detect whether a comment becomes inconsistent as a result of changes to the corresponding body of code, in order to catch potential inconsistencies just-in-time, i.e., before they are committed to a code base. To achieve this, we develop a deep-learning approach that learns to correlate a comment with code changes. By evaluating on a large corpus of comment/code pairs spanning various comment types, we show that our model outperforms multiple baselines by significant margins. For extrinsic evaluation, we show the usefulness of our approach by combining it with a comment update model to build a more comprehensive automatic comment maintenance system which can both detect and resolve inconsistent comments based on code changes.Comment: Accepted in AAAI 202

Associating Natural Language Comment and Source Code Entities

Comments are an integral part of software development; they are natural language descriptions associated with source code elements. Understanding explicit associations can be useful in improving code comprehensibility and maintaining the consistency between code and comments. As an initial step towards this larger goal, we address the task of associating entities in Javadoc comments with elements in Java source code. We propose an approach for automatically extracting supervised data using revision histories of open source projects and present a manually annotated evaluation dataset for this task. We develop a binary classifier and a sequence labeling model by crafting a rich feature set which encompasses various aspects of code, comments, and the relationships between them. Experiments show that our systems outperform several baselines learning from the proposed supervision.Comment: Accepted in AAAI 202

Long-term treatment with galcanezumab in patients with chronic migraine: results from the open-label extension of the REGAIN study

Galcanezumab; Chronic migraine; Preventive treatmentGalcanezumab; Migraña crónica; Tratamiento preventivoGalcanezumab; Migranya crònica; Tractament preventiuBackground Galcanezumab, a monoclonal antibody to calcitonin gene-related peptide, was found to be safe and efficacious for the preventive treatment of chronic migraine based on the randomized, placebo-controlled double-blind period of the REGAIN study. Long-term safety and efficacy were assessed in an open-label extension. Methods Patients 18–65 years old with chronic migraine completing the 3-month double-blind period of REGAIN could enter a 9-month open-label extension (OLE; months 4–12). Upon entering the OLE, patients received a 240-mg galcanezumab loading dose, then 120 mg at the next month, with flexible dosing thereafter (120 or 240 mg/month). The primary efficacy measure was the mean change in the number of monthly migraine headache days from double-blind baseline to month 12. Other endpoints included response rates (based on percent reduction in monthly migraine headache days from double-blind baseline to month 12), safety and tolerability. Results Of patients who completed double-blind treatment, 1022 (99%) entered the OLE, with 81% completing month 12. From a baseline of 19.4 monthly migraine headache days at the beginning of the double-blind period, patients at month 12 in the previous placebo, 120-mg, and 240-mg galcanezumab groups had a mean change of −8.5, −9.0, and −8.0, respectively (SE = 0.43 to 0.55, within-group p’s < .001). At month 12, the percentage of patients with ≥50% response was 57%, 57%, and 53%, respectively. Percentage with ≥75% response was 32%, 31%, and 30%, respectively. Percentage with 100% response was 8%, 6%, and 6%, respectively. There were no significant new safety findings during the open-label period. The incidence of discontinuation from the OLE due to adverse events was 5%. Conclusion Galcanezumab was effective, safe, and well-tolerated, with high adherence, for up to 12 months of treatment in patients with chronic migraine

Conserving unprotected important coastal habitats in the Yellow Sea:Shorebird occurrence, distribution and food resources at Lianyungang

The Yellow Sea coastline in East Asia, an important staging area for migratory shorebirds in the East Asian-Australasian Flyway (EAAF), is rapidly deteriorating. Conserving the declining shorebird populations that rely on the Yellow Sea requires habitat protection and management based on sound ecological knowledge, especially on the seasonal occurrence of shorebirds, their daily movements and their food resources. However, in this region such ecological data are scarce, and expertise to collect them are less-established. Here we gather and assimilate such information for the coastal wetlands at Lianyungang on the Chinese Yellow Sea coast, an understudied and unprotected area where we found 27% of intertidal soft sediment habitats have been destroyed in 2003–2018 by reclamation. In 2008–2018, 43 shorebird species were recorded along this coastline, including 12 globally threatened or ‘Near Threatened’ species. In terms of number of shorebird species exceeding 1% of the EAAF population, with 22 species meeting this criterion, Lianyungang ranks highest among the >300 shorebird sites in East Asia. The benthic mollusc community of the intertidal flats were dominated by small soft-shelled bivalve species at very high densities, including 9399 individuals/m2 of <i>Potamocorbula laevis</i>, which are high-quality food for shorebirds to refuel during migration. Satellite tracked bar-tailed godwits (<i>Limosa lapponica</i>) and great knots (<i>Calidris tenuirostris</i>) stopped at Lianyungang for 5–30 days during northward and southward migration. The tidal movements of satellite-tagged birds indicated high-tide roosts and low-tide foraging areas, some of which are inaccessible on-ground. These movements can also be used to evaluate whether roosts and foraging areas are close enough to each other, and direct where to create new roost sites. Potential measures to increase the capacity of Lianyungang to support shorebirds include reducing human disturbances, creating roosts at undeveloped parts of the reclaimed land, and removing recently-built sea dikes to restore intertidal flats

Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain

Additional file 3. Fermentation profiles of Y133 and Y133-IIL in the presence of 1 % [BMIM]Cl at pH 6.5 and pH 5.0, and either aerobic or anaerobic conditions (n = 3, Mean ± S.E, except n = 2 for Y133 pH 6.5 anaerobic 72 h)

TIM-family Proteins Promote Infection of Multiple Enveloped Viruses through Virion-associated Phosphatidylserine

Human T-cell Immunoglobulin and Mucin-domain containing proteins (TIM1, 3, and 4) specifically bind phosphatidylserine (PS). TIM1 has been proposed to serve as a cellular receptor for hepatitis A virus and Ebola virus and as an entry factor for dengue virus. Here we show that TIM1 promotes infection of retroviruses and virus-like particles (VLPs) pseudotyped with a range of viral entry proteins, in particular those from the filovirus, flavivirus, New World arenavirus and alphavirus families. TIM1 also robustly enhanced the infection of replication-competent viruses from the same families, including dengue, Tacaribe, Sindbis and Ross River viruses. All interactions between TIM1 and pseudoviruses or VLPs were PS-mediated, as demonstrated with liposome blocking and TIM1 mutagenesis experiments. In addition, other PS-binding proteins, such as Axl and TIM4, promoted infection similarly to TIM1. Finally, the blocking of PS receptors on macrophages inhibited the entry of Ebola VLPs, suggesting that PS receptors can contribute to infection in physiologically relevant cells. Notably, infection mediated by the entry proteins of Lassa fever virus, influenza A virus and SARS coronavirus was largely unaffected by TIM1 expression. Taken together our data show that TIM1 and related PS-binding proteins promote infection of diverse families of enveloped viruses, and may therefore be useful targets for broad-spectrum antiviral therapies

Authoritarianism in the Living Room: Everyday Disciplines, Senses, and Morality in Taiwan’s Military Villages

With the nationalist government – Kuomintang (KMT) – retreating from mainland China in 1949, some 600,000 military personnel relocated to Taiwan. The military seized former Japanese colonial properties and built its own settlements, establishing temporary military dependents’ villages called juancun (眷村). When the prospect of counter-attacking the mainland vanished, the KMT had to face the reality of settling permanently in Taiwan. How, then, did the KMT’s authoritarian power enter the everyday lives of its own support group? In this article I will focus on the coercive elements of KMT authoritarianism, which permeated these military villages in Taiwan. I will look at the coercive mechanisms through the analytical lens of Foucauldian discipline. I argue that disciplinary techniques such as surveillance, disciplining of the body and the senses, as well as the creation of morality regimes played an important role in the cooptation of village residents into KMT authoritarianism by normalising and naturalising it