bluuebunny/crossref_metadata_2025 huggingface dataset:
Rat model of smoke inhalation-induced acute lung injury
Authors: Leiphrakpam Premila Devi , Weber Hannah R , Ogun Tobi , Buesing Keely L
Published: July 2021

Background

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a lethal disease with limited therapeutic options and an unacceptably high mortality rate. Understanding the complex pathophysiological processes involved in the development of ALI/ARDS is critical for developing novel therapeutic strategies. Smoke inhalation (SI) injury is the leading cause of morbidity and mortality in patients with burn-associated ALI/ARDS; however, to our knowledge few reliable, reproducible models are available for pure SI animal model to investigate therapeutic options for ALI/ARDS without the confounding variables introduced by cutaneous burn or other pathology.

Objective

To develop a small animal model of pure SI-induced ALI and to use this model for eventual testing of novel therapeutics for ALI.

Methods

Rats were exposed to smoke using a custom-made smoke generator. Peripheral oxygen saturation (SpO2), heart rate, arterial blood gas, and chest X-ray (CXR) were measured before and after SI. Wet/dry weight (W/D) ratio, lung injury score and immunohistochemical staining of cleaved caspase 3 were performed on harvested lung tissues of healthy and SI animals.

Results

The current study demonstrates the induction of ALI in rats after SI as reflected by a significant, sustained decrease in SpO2and the development of diffuse bilateral pulmonary infiltrates on CXR. Lung tissue of animals exposed to SI showed increased inflammation, oedema and apoptosis as reflected by the increase in W/D ratio, injury score and cleaved caspase 3 level of the harvested tissues compared with healthy animals.

Conclusion

We have successfully developed a small animal model of pure SI-induced ALI. This model is offered to the scientific community as a reliable model of isolated pulmonary SI-induced injury without the confounding variables of cutaneous injury or other systemic pathology to be used for study of novel therapeutics or other investigation.
First-line avelumab in a cohort of 116 patients with metastatic Merkel cell carcinoma (JAVELIN Merkel 200): primary and biomarker analyses of a phase II study
Authors: D'Angelo Sandra P , Lebbé Celeste , Mortier Laurent , Brohl Andrew S , Fazio Nicola , Grob Jean-Jacques , Prinzi Natalie , Hanna Glenn J , Hassel Jessica C , Kiecker Felix , Georges Sara , Ellers-Lenz Barbara , Shah Parantu , Güzel Gülseren , Nghiem Paul
Published: July 2021

Background

Avelumab (anti-programmed death ligand 1 (PD-L1)) is approved in multiple countries for the treatment of metastatic Merkel cell carcinoma (mMCC), a rare and aggressive skin cancer. We report efficacy and safety data and exploratory biomarker analyses from a cohort of patients with mMCC treated with first-line avelumab in a phase II trial.

Methods

Patients with treatment-naive mMCC received avelumab 10 mg/kg intravenously every 2 weeks. The primary endpoint was durable response, defined as objective response (complete or partial response; assessed by independent review) lasting ≥6 months. Additional assessments included progression-free survival (PFS), overall survival (OS), safety, and biomarker analyses.

Results

In 116 patients treated with avelumab, median follow-up was 21.2 months (range: 14.9–36.6). Thirty-five patients had a response lasting ≥6 months, giving a durable response rate of 30.2% (95% CI: 22.0% to 39.4%). The objective response rate was 39.7% (95% CI: 30.7% to 49.2%). Median PFS was 4.1 months (95% CI: 1.4 to 6.1) and median OS was 20.3 months (95% CI: 12.4 to not estimable). Response rates were numerically higher in patients with PD-L1+ tumors, Merkel cell polyomavirus (MCPyV)-negative tumors, and tumors with increased intratumoral CD8+T-cell density. Exploratory analyses did not identify a biomarker that could reliably predict a response to first-line treatment with avelumab; however, a novel gene expression signature to identify the presence of MCPyV+ tumors was derived. Treatment-related adverse events (any grade) occurred in 94 (81.0%) patients, including grade 3/4 events in 21 (18.1%) patients; no treatment-related deaths occurred.

Conclusion

In patients with mMCC, first-line treatment with avelumab led to responses in 40% and durable responses in 30%, and was associated with a low rate of grade 3/4 treatment-related adverse events.
Corticobasal syndrome: a practical guide
Authors: Wilson Duncan , Le Heron Campbell , Anderson Tim
Published: July 2021

Corticobasal syndrome is a disorder of movement, cognition and behaviour with several possible underlying pathologies, including corticobasal degeneration. It presents insidiously and is slowly progressive. Clinicians should consider the diagnosis in people presenting with any combination of extrapyramidal features (with poor response to levodopa), apraxia or other parietal signs, aphasia and alien-limb phenomena. Neuroimaging showing asymmetrical perirolandic cortical changes supports the diagnosis, while advanced neuroimaging may give insight into the underlying pathology. Identifying corticobasal syndrome carries some management implications (especially if protein-based treatments arise in the future) and prognostic significance. Its treatment is largely symptomatic and is best undertaken within a multidisciplinary setting, including a neurologist, physiotherapist, occupational therapist, speech language therapist, psychiatrist and, ultimately, a palliative care clinician. Corticobasal syndrome can be a confusing entity for neurologists, not least because it has over time evolved from being considered predominantly as a movement disorder to a condition spanning a wide range of cognitive and motor manifestations. In this practical review, we attempt to disentangle this syndrome and provide clarity around diagnosis, its underlying pathological substrates, key clinical features and potential treatments.
Association of the dysfunctional placentation endotype of prematurity with bronchopulmonary dysplasia: a systematic review, meta-analysis and meta-regression
Authors: Pierro Maria , Villamor-Martinez Eduardo , van Westering-Kroon Elke , Alvarez-Fuente Maria , Abman Steven H , Villamor Eduardo
Published: July 2021

Background

Antenatal pathological conditions are key in the pathogenesis of bronchopulmonary dysplasia (BPD). Pathophysiological pathways or endotypes leading to prematurity and perinatal lung injury can be clustered into two groups: infection and dysfunctional placentation, which include hypertensive disorders of pregnancy (HDP) and intrauterine growth restriction (IUGR). We conducted a systematic review of observational studies exploring the association between the dysfunctional placentation endotype and BPD.

Methods

MEDLINE, Embase and Web of Science databases were searched up to February 2020 for studies reporting data on the diagnosis of HDP, IUGR or small for gestational age (SGA) and BPD risk. BPD was classified as BPD28 (supplemental oxygen on day 28), BPD36 (oxygen at 36 weeks postmenstrual age), severe BPD (≥ 30% oxygen or mechanical ventilation), BPD36/death and BPD-associated pulmonary hypertension.

Results

Of 6319 studies screened, 211 (347 963 infants) were included. Meta-analysis showed an association between SGA/IUGR and BPD36 (OR 1.56, 95% CI 1.37 to 1.79), severe BPD (OR 1.82, 95% CI 1.36 to 2.29) and BPD/death (OR 1.91, 95% CI 1.55 to 2.37). Exposure to HDP was not associated with BPD but was associated with decreased odds of BPD/death (OR 0.77, 95% CI 0.64 to 0.94). Both HDP (OR 1.41, 95% CI 1.10 to 1.80) and SGA/IUGR (OR 2.37, 95% CI 1.86 to 3.02) were associated with BPD-associated pulmonary hypertension.

Conclusion

When placental vascular dysfunction is accompanied by fetal growth restriction or being born SGA, it is associated with an increased risk of developing BPD and pulmonary hypertension. The placental dysfunction endotype of prematurity is strongly associated with the vascular phenotype of BPD.

Prospero registration number

Review protocol was registered in PROSPERO database (ID=CRD42018086877).
Burden of nosocomial COVID-19 in Wales: results from a multicentre retrospective observational study of 2508 hospitalised adults
Authors: Ponsford Mark J , Jefferies Rhys , Davies Chris , Farewell Daniel , Humphreys Ian R , Jolles Stephen , Fairbairn Sara , Lewis Keir , Menzies Daniel , Benjamin Amit , Thaivalappil Favas , Williams Chris , Barry Simon M
Published: July 2021

The burden of nosocomial SARS-CoV-2 infection remains poorly defined. We report on the outcomes of 2508 adults with molecularly-confirmed SARS-CoV-2 admitted across 18 major hospitals, representing over 60% of those hospitalised across Wales between 1 March and 1 July 2020. Inpatient mortality for nosocomial infection ranged from 38% to 42%, consistently higher than participants with community-acquired infection (31%–35%) across a range of case definitions. Those with hospital-acquired infection were older and frailer than those infected within the community. Nosocomial diagnosis occurred a median of 30 days following admission (IQR 21–63), suggesting a window for prophylactic or postexposure interventions, alongside enhanced infection control measures.
The let-7f-5p–Nme4 pathway mediates tumor necrosis factor α-induced impairment in osteogenesis of bone marrow-derived mesenchymal stem cells
Authors: Zhao Ying-Jie , Gao Zheng-Chao , He Xi-Jing , Li Jing
Published: July 2021

Although tumor necrosis factor α (TNF-α)-mediated inflammation significantly impacts osteoporosis, the mechanisms underlying the osteogenic differentiation defects of bone marrow-derived mesenchymal stem cells (BM-MSCs) caused by TNF-α remain poorly understood. We found that TNF-α stimulation of murine BM-MSCs significantly upregulated the expression levels of several microRNAs (miRNAs), including let-7f-5p, but this increase was significantly reversed by treatment with the kinase inhibitor BAY 11-7082. To study gain- or loss of function, we transfected cells with an miRNA inhibitor or miRNA mimic. We then demonstrated that let-7f-5p impaired osteogenic differentiation of BM-MSCs in the absence and presence of TNF-α, as evidenced by alkaline phosphatase and alizarin red staining as well as quantitative assays of the mRNA levels of bone formation marker genes in differentiated BM-MSCs. Moreover, let-7f-5p targets the 3′ untranslated region of Nucleoside diphosphate kinase 4 (Nme4) mRNA and negatively regulates Nme4 expression in mouse BM-MSCs. Ectopic expression of Nme4 completely reversed the inhibitory effects of the let-7f-5p mimic on osteogenic differentiation of mouse BM-MSCs. Furthermore, inhibition of let-7f-5p or overexpression of Nme4 in BM-MSCs restored in-vivo bone formation in an ovariectomized animal model. Collectively, our work indicates that let-7f-5p is involved in TNF-α-mediated reduction of BM-MSC osteogenesis via targeting Nme4.
Spring diet of American black bears (Ursus americanus) in a moose (Alces alces) – woodland caribou (Rangifer tarandus caribou) system in northern Ontario, Canada
Authors: McLaren A.A.D. , Jamieson S.E. , Bond M. , Rodgers A.R. , Patterson B.R.
Published: July 2021

American black bears (Ursus americanus Pallas, 1780) are opportunistic foragers, and across most of their range in North America, their diet is predominantly vegetation with limited consumption of vertebrates and invertebrates. However, they are also predators of ungulates, especially neonates, with regional variation in the amount of predation pressure they exert. We used scat analysis to examine the diet of black bears during the calving season in a moose (Alces alces (Linnaeus, 1758)) – woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)) system in the Boreal forest of northern Ontario, Canada. Bears consumed herbaceous plants (46.5%), fruits and (or) seeds (20.0%), moose (3.3% adults; 4.3% calves), American beaver (Castor canadensis Kuhl, 1820; 8.5%), and insects (mostly ants; 4.2%). Bears had the highest consumption of moose and beaver in early spring, before switching to a more vegetation-dominated diet. We did not detect evidence of caribou consumption. Based on our results, black bear consumption of moose, particularly neonates, may warrant further investigation.
A Fourier-cumulant analysis for multiharmonic flow fluctuation
Authors: Taghavi Seyed Farid
Published: July 2021

The Fourier analysis of the final particle distribution followed by cumulant study of the Fourier coefficient event-by-event fluctuation is one of the main approaches for testing the collective evolution in the heavy-ion collision. Using a multidimensional generating function, we propose a method to extract any possible cumulant of multiharmonic flow fluctuations and classify them in terms of the order of cumulants and harmonics involved in them. In particular, we show that there are 33 distinct cumulants with order 2, 3, 4, 5 and harmonics 2, 3, 4, 5. We compute the normalized version of these cumulants from hydrodynamic simulation for Pb–Pb collisions based on$$_\mathtt{R}$$R++. We compare the simulation with those normalized cumulants that the LHC has measured and predict the unmeasured ones. Comparing the initial and final state fluctuation normalized cumulants, we compute the linear and nonlinear hydrodynamic response couplings. We finally introduce the genuine three-particle correlation function containing information of all third-order cumulants.
Virial theorem in scalar tensor fourth order gravity
Authors: Capolupo A. , Lambiase G. , Stabile A. , Stabile An.
Published: July 2021

In this paper, we study, in the Newtonian limit, the virial theorem in the context of a scalar tensor fourth order gravity. In particular, we show, that for a isolated galaxy in viral equilibrium, a specific class of scalar tensor fourth order gravity, i.e. $$f(R,\phi )+\omega (\phi )\,\phi _{;\alpha }\,\phi ^{;\alpha }$$

f

(
R
,
ϕ
)

+
ω

(
ϕ
)

ϕ

;
α

ϕ

;
α

in not suitable to explain the large fraction of dark matter necessary to have the flatness of the galaxies rotation curves experimentally observed.
The cryogenic control system of SHINE
Authors: Jiang Geyang , Ni Qing , Wang Shuhua , Sun Jiuce , Ouyang Zhengrong , Zhang Lei , Tong Zilei , Wang Yi
Published: July 2021

The Shanghai High repetition rate XFEL and Extreme Light Facility (SHINE), an advanced XFEL project, is now being built at Shanghai Advanced Research Institute (SARI), Chinese Academy of Sciences. It includes a hard X-ray free electron laser and a 100 pW intense laser facilities with overall length of 3.1 km. The XFEL part including an 8 GeV LINAC and 3 undulator lines is cooled with forced superfluid and supercritical helium at 2 K/4 K. The cryogenic system of SHINE consists of test facility cryogenic system (TFCS), accelerator cryogenic system (ACCS), and undulator cryogenic system (UNCS). A dedicated control system based on Experimental Physics and Industrial Control System (EPICS) will be built to automate the cryogenic system with process control, PID control loops, real-time data acquisition and storage, alarm handler and human machine interface. It is capable of automatic recovery as well. This paper describes details of control system structure, interfaces, controllers and the integration under EPICS framework.
Feasibility study of TPC detector at high luminosity Z pole on the circular collider
Authors: Yuan Zhiyang , Qi Huirong , Chang Yue , Zhang Jian , Wu Ye , Zhang Hongyu , Chen Yuanbo , Cai Yiming , Li Yulan , Deng Zhi , Gong Hui
Published: July 2021

With the development of the circular collider, it is necessary to make accurate physics experimental measurements of particle properties at higher luminosity [Formula: see text] pole. Micro-pattern gaseous detectors (MPGDs), which contain gaseous electron multiplier (GEM) and micro-mesh gaseous structures (Micromegas), have excellent potential for development as the readout devices of the time projection chamber (TPC) tracker detector. To meet the updated physics requirements of the high luminosity [Formula: see text] from the preliminary concept design report (preCDR) to concept design report (CDR) at the circular electron–positron collider (CEPC). In this paper, the space charge distortion of the TPC detector is simulated with the CEPC beam structure. Using the multi-physics simulation software package, the distribution of ion estimated by Geant4 is used as the input for the differential equation, and the relationship between the ion density distribution and electric field in the detector chamber is simulated. These simulation results show that the maximum deviation for Higgs [Formula: see text] meets the performance requirements in CEPC TPC detector at the high luminosity [Formula: see text] pole, while it is still a considerable challenge for [Formula: see text] pole, with the maximum deviation [Formula: see text]. According to the previous developments, the cascaded structure of GEM and Micromegas detector has been measured. The new considerations of the detector’s requirements were given, the gain needs to be reached to about 2000 with IBF[Formula: see text]Gain under 0.1, and IBF means the ions back flow ratio of the detector. The pixel TPC is a potential option to replace the traditional MPGDs with the low gain, low occupancy, and outstanding pattern recognition. Finally, some update parameters and experiments results were compared.
A two-nearest-neighbor structure model and analysis of low-expansion Fe–Ni alloys
Authors: Hong Hai-Lian , Gao Hao , Yang Chi-Hsin , Wang Kun-Chieh , Yan Hui-Xian
Published: July 2021

The main goal of the study is to introduce a two-nearest-neighbor structure model for analyzing low-expansion Fe–Ni alloys. A two-shell atomic structure model is proposed to accurately locate the compositions of the alloy. In the presented model, the Cowley parameters of the alloy short-range ordered structure are considered. The selection of the first-nearest-neighbor cluster is determined, and the number and composition ratio of the second-nearest-neighbor atoms are evaluated by means of the spherical periodic oscillation model. The results show that the developed formula can provide a practical procedure for the composition design of low-expansion Fe–Ni alloys.
Transport through several four-quantum-dot topological structures
Authors: Zhi Qingshuang , Chen Kongfa , He Zelong
Published: July 2021

In this paper, several four-quantum-dot topological structures are designed. The influence of the interdot coupling strength and intradot Coulomb interactions on the conductance is discussed. The location of the anti-resonance band can be manipulated by tuning the interdot coupling strength, which suggests a physical scheme of an effective quantum switch. The Fano anti-resonance peak may evolve into a resonance peak. For the particular value of the interdot coupling strength, two Fano anti-resonances collapse and bound states in the continuum are formed. Moreover, many-body effect makes the number of anti-resonance bands increase. This study provides a theoretical basis for the design of quantum computing devices.
Novel quantum group signature scheme based on orthogonal product states
Authors: Jiang Donghuan , Yuan Fei , Xu Guangbao
Published: July 2021

In this paper, we present a quantum group signature (QGS) scheme based on orthogonal product states (OPSs) that cannot be perfectly distinguished by local operations and classical communication. Our scheme has all the properties of QGS, including unforgeability, undeniability, traceability, verifiability and anonymity. These properties can guarantee the security of the scheme. More importantly, different particles of a product state that comes from a nonlocal set are transmitted separately, thus the information that is encoded in the product state will not be leaked. Security and efficiency analysis of the scheme show that our scheme is secure and efficient.
Nonlinear Optical Properties and Cytotoxicity Studies of Fruit Extract Synthesized Silver and Gold Nanostructures
Authors: Ramya E. , Jyothi L. , Desai Narayana Rao
Published: July 2021

Eco-friendlybiosynthesis of silver nanoparticles (Ag NPs) and gold (Au NPs) nanoparticles by using Punica granatum and C. reticulata extracts were synthesized efficiently. Ag and Au NPs with sizes 8–10 nm and 30–40 nm were successfully synthesized and extracts serve as capping agents. Forming of NPs was confirmed through UV-visible spectra, transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier transform infrared spectra (FTIR) studies. The effect of NPs on the luminescence of Eu(TTFA)3and Sm(TTFA)3complexes was investigated. Luminescence intensities of the complexes were enhanced several times in the presence of silver and get quenched due to reabsorption of Au NPs. The nonlinear optical properties of NPs were calculated using open aperture Z-scan and degenerate four-wave mixing in the femtosecond region. The toxicity and antimicrobial activities of Ag and Au NPs were studied.
The quantum disk is not a quantum group
Authors: Krajczok Jacek , Sołtan Piotr M.
Published: July 2021

In this paper, we show that the quantum disk, i.e. the quantum space corresponding to the Toeplitz [Formula: see text]-algebra does not admit any compact quantum group structure. We prove that if such a structure existed the resulting compact quantum group would simultaneously be of Kac type and not of Kac type. The main tools used in the solution come from the theory of operators on Hilbert spaces.
Near real-time management of spectral interferences with portable X-ray fluorescence spectrometers: application to Sc quantification in nickeliferous laterite ores
Authors: Lacroix Elodie , Cauzid Jean , Teitler Yoram , Cathelineau Michel
Published: July 2021

Since the development of portable X-ray fluorescence (pXRF) spectrometers, few studies have been conducted on the influence of spectral interferences between chemical elements. This study aims to improve the management of these interferences to obtain more reliable geochemical analyses. We specifically investigate Ca-related interferences on Sc analysis for the case of Ni-rich laterite samples using the Niton XL3t GOLDD + pXRF analyser. Three quantification methods were tested on 59 pelletized samples using the ‘Soil’ mode. The first, named ‘Manufacturer’, represents the elemental quantification directly provided by the device based on regions of interest and multilinear corrections of spectral interferences configured during the spectrometer design. The second, the ‘20 Cu’ method, is based on spectral fitting using the PyMCA software. The third, the ‘18 Fe’ method, combines spectral fitting with modified experimental conditions. For each, a quantification methodology was developed, establishing (i) Ca and Sc calibration lines and (ii) Ca/Sc threshold values delimiting fields of ‘reliable’, ‘to be confirmed’ and ‘unreliable’ measurements. The ‘20 Cu’ and ‘18 Fe’ methods greatly extend the ‘reliable measurements’ field concerning the Ca/Sc ratio compared to the ‘Manufacturer’ method. The ‘18 Fe’ method was also found to provide the most negligible measurement dispersion.

Supplementary material:
Figures A–F and Tables A and B are available at
https://doi.org/10.6084/m9.figshare.c.5511838
When and How to Make Breaking Changes
Authors: Bogart Chris , Kästner Christian , Herbsleb James , Thung Ferdian
Published: July 2021

Open source software projects often rely on package management systems that help projects discover, incorporate, and maintain dependencies on other packages, maintained by other people. Such systems save a great deal of effort over ad hoc ways of advertising, packaging, and transmitting useful libraries, but coordination among project teams is still needed when one package makes a breaking change affecting other packages. Ecosystems differ in their approaches to breaking changes, and there is no general theory to explain the relationships between features, behavioral norms, ecosystem outcomes, and motivating values. We address this through two empirical studies. In an interview case study, we contrast Eclipse, NPM, and CRAN, demonstrating that these different norms for coordination of breaking changes shift the costs of using and maintaining the software among stakeholders, appropriate to each ecosystem’s mission. In a second study, we combine a survey, repository mining, and document analysis to broaden and systematize these observations across 18 ecosystems. We find that all ecosystems share values such as stability and compatibility, but differ in other values. Ecosystems’ practices often support their espoused values, but in surprisingly diverse ways. The data provides counterevidence against easy generalizations about why ecosystem communities do what they do.
Eagle
Authors: Lu Jingbo , He Dongjie , Xue Jingling
Published: July 2021

Object sensitivity is widely used as a context abstraction for computing the points-to information context-sensitively for object-oriented programming languages such as Java. Due to the combinatorial explosion of contexts in large object-oriented programs,
k
-object-sensitive pointer analysis (under
k
-limiting), denoted

k
-obj

, is often inefficient even when it is scalable for small values of
k
, where
k
⩽ 2 holds typically. A recent popular approach for accelerating

k
-obj

trades precision for efficiency by instructing

k
-obj

to analyze only some methods in a program context-sensitively, determined heuristically by a pre-analysis. In this article, we investigate how to develop a fundamentally different approach,
Eagle
, for designing a pre-analysis that can make

k
-obj

run significantly faster while maintaining its precision. The novelty of
Eagle
is to enable

k
-obj

to analyze a method with partial context sensitivity (i.e., context-sensitively for only some of its selected variables/allocation sites) by solving a context-free-language (CFL) reachability problem based on a new CFL-reachability formulation of

k
-obj

. By regularizing one CFL for specifying field accesses and using another CFL for specifying method calls, we have formulated
Eagle
as a fully context-sensitive taint analysis (without
k
-limiting) that is both effective (by selecting the variables/allocation sites to be analyzed by

k
-obj

context-insensitively so as to reduce the number of context-sensitive facts inferred by

k
-obj

in the program) and efficient (by running linearly in terms of the number of pointer assignment edges in the program). As
Eagle
represents the first precision-preserving pre-analysis, our evaluation focuses on demonstrating its significant performance benefits in accelerating

k
-obj

for a set of popular Java benchmarks and applications, with call graph construction, may-fail-casting, and polymorphic call detection as three important client analyses.
Automatically Identifying the Quality of Developer Chats for Post Hoc Use
Authors: Chatterjee Preetha , Damevski Kostadin , Kraft Nicholas A. , Pollock Lori
Published: July 2021

Software engineers are crowdsourcing answers to their everyday challenges on Q&A forums (e.g., Stack Overflow) and more recently in public chat communities such as Slack, IRC, and Gitter. Many software-related chat conversations contain valuable expert knowledge that is useful for both mining to improve programming support tools and for readers who did not participate in the original chat conversations. However, most chat platforms and communities do not contain built-in quality indicators (e.g., accepted answers, vote counts). Therefore, it is difficult to identify conversations that contain useful information for mining or reading, i.e., conversations of post hoc quality. In this article, we investigate automatically detecting developer conversations of post hoc quality from public chat channels. We first describe an analysis of 400 developer conversations that indicate potential characteristics of post hoc quality, followed by a machine learning-based approach for automatically identifying conversations of post hoc quality. Our evaluation of 2,000 annotated Slack conversations in four programming communities (python, clojure, elm, and racket) indicates that our approach can achieve precision of 0.82, recall of 0.90, F-measure of 0.86, and MCC of 0.57. To our knowledge, this is the first automated technique for detecting developer conversations of post hoc quality.
Speeding Up Data Manipulation Tasks with Alternative Implementations
Authors: Tao Yida , Tang Shan , Liu Yepang , Xu Zhiwu , Qin Shengchao
Published: July 2021

As data volume and complexity grow at an unprecedented rate, the performance of data manipulation programs is becoming a major concern for developers. In this article, we study how alternative API choices could improve data manipulation performance while preserving task-specific input/output equivalence. We propose a lightweight approach that leverages the comparative structures in Q&A sites to extracting alternative implementations. On a large dataset of Stack Overflow posts, our approach extracts 5,080 pairs of alternative implementations that invoke different data manipulation APIs to solve the same tasks, with an accuracy of 86%. Experiments show that for 15% of the extracted pairs, the faster implementation achieved >10x speedup over its slower alternative. We also characterize 68 recurring alternative API pairs from the extraction results to understand the type of APIs that can be used alternatively. To put these findings into practice, we implement a tool,
AlterApi7
, to automatically optimize real-world data manipulation programs. In the 1,267 optimization attempts on the Kaggle dataset, 76% achieved desirable performance improvements with up to orders-of-magnitude speedup. Finally, we discuss notable challenges of using alternative APIs for optimizing data manipulation programs. We hope that our study offers a new perspective on API recommendation and automatic performance optimization.
Armed Cats
Authors: Alglave Jade , Deacon Will , Grisenthwaite Richard , Hacquard Antoine , Maranget Luc
Published: July 2021

We report on the process for formal concurrency modelling at Arm. An initial formal consistency model of the Arm achitecture, written in the cat language, was published and upstreamed to the herd+diy tool suite in 2017. Since then, we have extended the original model with extra features, for example, mixed-size accesses, and produced two provably equivalent alternative formulations.

In this article, we present a comprehensive review of work done at Arm on the consistency model. Along the way, we also show that our principle for handling mixed-size accesses applies to x86: We confirm this via vast experimental campaigns. We also show that our alternative formulations are applicable to any model phrased in a style similar to the one chosen by Arm.
Software Architectural Migration
Authors: Chondamrongkul Nacha , Sun Jing , Warren Ian
Published: July 2021

Software architectural designs are usually changed over time to support emerging technologies and to adhere to new principles. Architectural migration is an important activity that helps to transform the architectural styles applied during a system’s design with the result of modernising the system. If not performed correctly, this process could lead to potential system failures. This article presents an automated approach to refactoring architectural design and to planning the evolution process. With our solution, the architectural design can be refactored, ensuring that system functionality is preserved. Furthermore, the architectural migration process allows the system to be safely and incrementally transformed. We have evaluated our approach with five real-world software applications. The results prove the effectiveness of our approach and identify factors that impact the performance of architectural verification and migration planning. An interesting finding is that planning algorithms generate migration plans that differ in term of their relative efficiency.
Bias-corrected Estimation of the Density of a Conditional Expectation in Nested Simulation Problems
Authors: Yang Ran , Kent David , Apley Daniel W. , Staum Jeremy , Ruppert David
Published: July 2021

Many two-level nested simulation applications involve the conditional expectation of some response variable, where the expected response is the quantity of interest, and the expectation is with respect to the inner-level random variables, conditioned on the outer-level random variables. The latter typically represent random risk factors, and risk can be quantified by estimating the probability density function (pdf) or cumulative distribution function (cdf) of the conditional expectation. Much prior work has considered a naïve estimator that uses the empirical distribution of the sample averages across the inner-level replicates. This results in a biased estimator, because the distribution of the sample averages is over-dispersed relative to the distribution of the conditional expectation when the number of inner-level replicates is finite. Whereas most prior work has focused on allocating the numbers of outer- and inner-level replicates to balance the bias/variance tradeoff, we develop a bias-corrected pdf estimator. Our approach is based on the concept of density deconvolution, which is widely used to estimate densities with noisy observations but has not previously been considered for nested simulation problems. For a fixed computational budget, the bias-corrected deconvolution estimator allows more outer-level and fewer inner-level replicates to be used, which substantially improves the efficiency of the nested simulation.
The Agile Success Model
Authors: Russo Daniel
Published: July 2021

Organizations are increasingly adopting Agile frameworks for their internal software development. Cost reduction, rapid deployment, requirements and mental model alignment are typical reasons for an Agile transformation. This article presents an in-depth field study of a large-scale Agile transformation in a mission-critical environment, where stakeholders’ commitment was a critical success factor. The goal of such a transformation was to implement mission-oriented features, reducing costs and time to operate in critical scenarios. The project lasted several years and involved over 40 professionals. We report how a hierarchical and plan-driven organization exploited Agile methods to develop a Command & Control (C2) system. Accordingly, we first abstract our experience, inducing a success model of general use for other comparable organizations by performing a post-mortem study. The goal of the inductive research process was to identify critical success factors and their relations. Finally, we validated and generalized our model through Partial Least Squares - Structural Equation Modelling, surveying 200 software engineers involved in similar projects. We conclude the article with data-driven recommendations concerning the management of Agile projects.
Collaboration in the IETF
Authors: Welzl Michael , Oepen Stephan , Jaskula Cezary , Griwodz Carsten , Islam Safiqul
Published: July 2021

RFC 9000, published in May 2021, marks an important milestone for the Internet's standardization body, the Internet Engineering Task Force (IETF): finally, the specification of the QUIC protocol is available. QUIC is the result of a five-year effort - and it is also the second of two major protocols (the first being SPDY, which later became HTTP/2) that Google LLC first deployed, and then brought to the IETF for standardization. This begs the question: when big players follow such a "shoot first, discuss later" approach, is IETF collaboration still "real", or is the IETF now being (mis-)used to approve protocols for standardization when they are already practically established, without really actively involving anyone but the main proponents?
Best Practices for the Design of Clinical Trials Related to the Visual System
Authors: Maguire Maureen G.
Published: July 2021

Clinical trials for conditions affecting the visual system need to not only conform to the guidelines for all clinical trials, but also accommodate the possibility of both eyes of a single patient qualifying for the trial. In this review, I present the interplay of the key components in the design of a clinical trial, along with the modifications or options that may be available for trials addressing ocular conditions. Examples drawn from published reports of the design and results of clinical trials of ocular conditions are provided to illustrate application of the design principles. Current approaches to data analysis and reporting of trials are outlined, and the oversight and regulatory procedures to protect participants in clinical trials are discussed.
Transport Phenomena in Low Temperature Lithium-Ion Battery Electrolytes
Authors: Ringsby Alexandra J. , Fong Kara D. , Self Julian , Bergstrom Helen K. , McCloskey Bryan D. , Persson Kristin A.
Published: July 2021

Lithium-ion batteries face low temperature performance issues, limiting the adoption of technologies ranging from electric vehicles to stationary grid storage. This problem is thought to be exacerbated by slow transport within the electrolyte, which in turn may be influenced by ion association, solvent viscosity, and cation transference number. How these factors collectively impact low temperature transport phenomena, however, remains poorly understood. Here we show using all-atom classical molecular dynamics (MD) simulations that the dominant factor influencing low temperature transport in LP57 (1 M LiPF6 in 3:7 ethylene carbonate (EC)/ethyl methyl carbonate (EMC)) is solvent viscosity, rather than ion aggregation or cation transference number. We find that ion association decreases with decreasing temperature, while the cation transference number is positive and roughly independent of temperature. In an effort to improve low temperature performance, we introduce γ-butyrolactone (GBL) as a low viscosity co-solvent to explore two alternative formulations: 1 M LiPF6 in 15:15:70 EC/GBL/EMC and 3:7 GBL/EMC. While GBL reduces solution viscosity, its low dielectric constant results in increased ion pairing, yielding neither improved bulk ionic conductivity nor appreciably altered ion transport mechanisms. We expect that these results will enhance understanding of low temperature transport and inform the development of superior electrolytes.
Notch2 suppression mimicking changes in human pulmonary hypertension modulates Notch1 and promotes endothelial cell proliferation
Authors: Sahoo Sanghamitra , Li Yao , de Jesus Daniel , Sembrat John , Rojas Mauricio M. , Goncharova Elena , Cifuentes-Pagano Eugenia , Straub Adam C. , Pagano Patrick J.
Published: July 2021

This study demonstrates a previously unidentified role for Notch2 in the maintenance of lung vascular endothelial cell quiescence and pulmonary artery hypertension (PAH). A key novel finding is that Notch2 suppression activates Notch1 via Rb-E2F1-mediated signaling and induces proliferation and apoptosis resistance in human pulmonary artery endothelial cells. Notably, PAH patients show reduced levels of endothelial Notch2 in their pulmonary arteries, supporting Notch2 as a fundamental driver of PAH pathogenesis.
Genetically determined exercise capacity affects systemic glucose response to insulin in rats
Authors: Schwarzer Michael , Molis Annika , Schenkl Christina , Schrepper Andrea , Britton Steven L. , Koch Lauren G. , Doenst Torsten
Published: July 2021

Aerobic exercise capacity is inversely related to morbidity and mortality as well as to insulin resistance. However, exercising in patients has led to conflicting results, presumably because aerobic exercise capacity consists of intrinsic (genetically determined) and extrinsic (environmentally determined) parts. The contribution of both parts to insulin sensitivity is also not clear. We investigated sedentary and exercised (aerobic interval training) high-capacity runners (HCR) and low-capacity runners (LCR) differing in their genetically determined aerobic exercise capacity to determine the contribution of both parts to insulin sensitivity. LCR and HCR differed in their untrained exercise capacity and body weight. Sedentary LCR displayed a diabetic phenotype with higher random glucose, lower glucose infusion rate during hyperinsulinemic euglycemic clamping than HCR. Echocardiography showed equal morphological and functional parameters and no change with exercise. Four week of exercise caused significant improvements in aerobic exercise capacity, which was more pronounced in LCR. However, with respect to glucose use, exercise affected HCR only. In these animals, exercise increased 2-deoxyglucose uptake in gastrocnemius (+58.5%, P = 0.1) and in epididymal fat (+106%; P < 0.05). Citrate synthase activity also increased in these tissues (gastrocnemius 69% epididymal fat 63%). In our model of HCR and LCR, genetic predisposition for low exercise capacity is associated with impaired insulin sensitivity and impedes exercise-induced improvements in insulin response. Our results suggest that genetic predisposition for low aerobic exercise capacity impairs insulin response, which may not be overcome by exercise.
Global Dynamics, Boundedness, and Semicycle Analysis of a Difference Equation
Authors: Khan Abdul Qadeer , El-Metwally Hamdy
Published: July 2021

In this paper, we explore local stability, attractor, periodicity character, and boundedness solutions of the second-order nonlinear difference equation. Finally, obtained results are verified numerically.
Applied Research on InSAR and GPS Data Fusion in Deformation Monitoring
Authors: Zhang Ziwen , Wang Xuelian , Wu Yongdong , Zhao Zengpeng , E Yang
Published: July 2021

With the enrichment of land subsidence monitoring means, data fusion of multisource land subsidence data has gradually become a research hotspot. The Interferometry Synthetic Aperture Radar (InSAR) is a potential Earth observation approach, and it has been verified to have a variety of applications in measuring ground movement, urban subsidence, and landslides but similar to Global Positioning System (GPS). The InSAR observation accuracy and measurements are affected by the tropospheric delay error as well as by the Earth’s ionospheric and tropospheric layers. In order to rectify the InSAR result, there is a need to interpolate the GPS-derived tropospheric delay. Keeping in view of the above, this research study has presented an improved Inverse Distance Weighting (IIDW) interpolation method based on Inverse Distance Weighting (IDW) interpolation by using Sentinel-1 radar satellite image provided by European Space Agency (ESA) and the measured data from the Continuously Operating Reference Stations (CORS) provided by the Survey and Mapping Office of the Lands Department of Hong Kong. Furthermore, the corrected differential tropospheric delay correction is used to correct the InSAR image. The experimental results show that the correction of tropospheric delay by IIDW interpolation not only improves the accuracy of Differential Interferometry Synthetic Aperture Radar (D-InSAR) but also provides a new idea for the solution of InSAR and GPS data fusion.
A Pilot Study Investigating the Expression Levels of Pluripotency-Associated Genes in Rectal Swab Samples for Colorectal Polyp and Cancer Diagnosis and Prognosis
Authors: Sin Ryan Wai-Yan , Foo Dominic Chi-Chung , Iyer Deepak Narayanan , Fan May Sau-Yee , Li Xue , Lo Oswens Siu-Hung , Law Wai-Lun , Ng Lui
Published: July 2021

Change in gene expression is inevitable in cancer development. With more studies demonstrating the contributions of cancer stem cells (CSCs) in colorectal cancer (CRC) development, this study is aimed at investigating whether rectal swab specimen serves as a tool for detection of dysregulation of CSC or stem cell (SC) markers and at evaluating its potential as a new promising screening method for high-risk patients. Expression levels of 15 pluripotency-associated genes were assessed by quantitative PCR in 53 rectal swab specimens referred for endoscopic screening. Dysregulated genes and joint panels based on such genes were examined for their diagnostic potentials for both polyp and CRC. Out of 15 genes, Oct4, CD26, c-MYC, and CXCR4 showed significantly differential expression among normal, polyp, and CRC patients. A panel of Oct4 and CD26 showed an AUC value of 0.80 (

p
=
0.003

) in identifying CRC patients from polyp/normal subjects, with sensitivity and specificity of 84.6% and 69.2%. A panel of c-MYC and CXCR4 achieved CRC/polyp identification with an AUC value of 0.79 (

p
=
0.002

), with a sensitivity of 82.8% and specificity of 80.0%. The sensitivity for polyp and CRC was 80.0% and 85.7%, respectively. Further analysis showed that higher c-MYC and CXCR4 level was detected in normal subjects who developed polyps after 5-6 years, in comparison with subjects with no lesion developed, and the AUC of the c-MYC and CXCR4 panel increased to 0.88 (

p
<
0.001

), with sensitivity and specificity of 84.4% and 92.3%, respectively, when these patients were included in the polyp group. This study suggests that the Oct4 and CD26 panel is a promising biomarker for distinguishing CRC from normal and polyp patients, whereas the c-MYC and CXCR4 panel may identify polyp and CRC from normal individuals.
[Retracted] Signal Recognition Based on APSO‐RBF Neural Network to Assist Athlete’s Competitive Ability Evaluation
Authors: Guo Feng , Huang Qingcheng
Published: July 2021

The advanced analysis and research methods of big data will provide theoretical support for the integration of athletes’ talent training. The advanced technological methods of big data will also give full play to the advantages of tapping the potential of talents and actively improve the success rate of grassroots young athletes. This paper proposes an improved Adaptive Particle Swarm Optimization (APSO) algorithm for the optimization of radial basis function (RBF) neural network parameters. The basic structure of RBF neural network is introduced, and the influence of parameters on the performance of RBF neural network is analyzed. The optimization method of RBF neural network parameters is analyzed, and Particle Swarm Optimization (PSO) algorithm is selected as the parameter optimization method of RBF neural network. In addition, an improved APSO algorithm is proposed according to the advantages and disadvantages of PSO and compared with other PSO algorithms. Experimental results show that the improved PSO algorithm has better accuracy. The improved PSO algorithm is applied to the parameter optimization of RBF neural network, and the experimental results prove the superiority of the proposed method. By weighting the second‐level indicators, the weights of the second‐level indicators of athletes’ competitive ability are in order of skill, athletic quality, psychological ability, and artistic expression. Skills are the main factors that determine the level of competitive ability. Sports quality and psychological ability are important guarantees for supporting the normal performance of skills. Artistic expressiveness is a supplementary factor for competitive ability. The various elements cooperate with each other and interact with each other. The indicators do not exist alone but cooperate with each other to support the formation of the entire athletic ability system. In the content of the competitive ability index of excellent athletes, technical ability is the core, and sports quality, psychological ability, and artistic performance ability ultimately exist to serve the improvement of technical ability. The competition scores of the 100 athletes counted in this article are all above 9.0 points. The difference between APSO‐RBF’s action quality scores of 100 athletes and the real value is less than 3%. In terms of movement difficulty, the APSO‐RBF evaluated athletes’ scores are close to 1.65 points, which is basically the same as the real value.