bluuebunny/crossref_metadata_2025 huggingface dataset:
The Phosphatidyl-
myo
-Inositol Dimannoside Acyltransferase PatA Is Essential for Mycobacterium tuberculosis Growth
In Vitro
and
In Vivo
Authors: Boldrin Francesca , Anso Itxaso , Alebouyeh Sogol , Sevilla Iker A. , Geijo Mariví , Garrido Joseba M. , Marina Alberto , Cioetto Mazzabò Laura , Segafreddo Greta , Guerin Marcelo E. , Manganelli Riccardo , Prados-Rosales Rafael
Published: January 2021

Tuberculosis (TB) is the leading cause of death from a single infectious agent. The emergence of drug resistance in strains of
M. tuberculosis
, the etiologic agent of TB, emphasizes the need to identify new targets and antimicrobial agents.
Assessment of Sample Pooling for Clinical SARS-CoV-2 Testing
Authors: Griesemer Sara B. , Van Slyke Greta , St. George Kirsten
Published: January 2021

Accommodating large increases in sample workloads has presented a major challenge to clinical laboratories during the coronavirus disease 2019 (COVID-19) pandemic. Despite the implementation of automated detection systems and previous efficiencies, including barcoding, electronic data transfer, and extensive robotics, capacities have struggled to meet the demand.
Complete Genome Sequence of
Bradyrhizobium
sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia
Authors: Oger-Desfeux Christine , Briolay Jérôme , Oger Philippe M. , Lafay Bénédicte
Published: January 2021

We report the complete genome sequence of
Bradyrhizobium
sp. strain BDV5040, representative of
Bradyrhizobium
genospecies B, which symbiotically associates with legume hosts belonging to all three Fabaceae subfamilies across the Australian continent. The complete genome sequence provides a genetic reference for this Australian genospecies.
Complete Genome Sequence of Rhizobium japonicum Podophage Pasto
Authors: Manuel Nikhil , Rushing Leika , Ravindran Aravind , Newkirk Heather , Burrowes Ben , Young Ry , Gonzalez Carlos
Published: January 2021

Rhizobium japonicum
is a Gram-negative bacterium of interest for research into nitrogen fixation in legumes. This article describes the isolation, sequencing, and annotation of
R. japonicum
podophage Pasto. While it shows no significant similarity to identified phages, genomic analysis indicates that Pasto may be temperate and is a novel T7-like podophage.
Influence of pre-existing structure on pluton emplacement and geomorphology: The Merrimac plutons, northern Sierra Nevada, California, USA
Authors: Langenheim V.E. , Vazquez J.A. , Schmidt K.M. , Guglielmo G. , Sweetkind D.S.
Published: January 2021

In much of the western Cordillera of North America, the geologic framework of crustal structure generated in the Mesozoic leaves an imprint on later plutonic emplacement, subsequent structural setting, and present landscape morphology. The Merrimac plutons in the northern Sierra Nevada (California, USA) are a good example of the influence of pre-existing structure at a larger scale. This paper updates and refines earlier studies of the Merrimac plutons, with the addition of analysis of gravity and magnetic data and new 206Pb/238U zircon dates. The gravity and magnetic data not only confirm the presence of two different neighboring plutons, but also (1) support the presence of a third pluton, (2) refine the nature of the contact between the Merrimac plutons as being structurally controlled, and (3) estimate the depth extent of the plutons to be ∼4–5 km. The zircon 206Pb/238U dates indicate that the two main plutons have statistically different crystallization ages nearly 4 m.y. apart. Geomorphic analyses, including estimates of relief, roughness and drainage density and generation of chi plots, indicate that the two main plutons are characterized by different elevations with large longitudinal channel knickpoints that we speculatively attribute to possible reactivation of pre-existing structure in addition to lithologic variations influencing relative erosion susceptibility in response to prior accelerated surface uplift.
Intravitreal ranibizumab for the management of serous maculopathy secondary to optic disc coloboma-associated choroidal neovascularisation
Authors: Schimansky Sarah , Wu Xia Ni , Egan Catherine , Mohamed Quresh
Published: January 2021

We report the case of a 19-year-old patient with symptomatic unilateral serous maculopathy associated with an optic nerve coloboma. Fluorescein angiography detected a focal late leak at the temporal edge of the coloboma which was later found to correspond with an area of choroidal neovascularisation on optical coherence tomography angiography. A course of intravitreal ranibizumab achieved good clinical and structural response. This report contributes to the evidence that maculopathies associated with cavitary optic nerve anomalies may in some instances result from choroidal neovascularisation. It also highlights the importance of angiography to identify potential choroidal neovascular membranes, particularly in the absence of haemorrhages and neovascular membranes on fundus examination and conventional optical coherence tomography.
Staphylococcus-associated acute glomerulonephritis in a patient with dermatomyositis
Authors: Sahoo Rasmi Ranjan , Pradhan Sourav , Goel Akhil Pawan , Wakhlu Anupam
Published: January 2021

Staphylococcus-associated glomerulonephritis (SAGN) occurs as a complication of staphylococcal infection elsewhere in the body. Dermatomyositis (DM) can be associated with glomerulonephritis due to the disease per se. We report a case of a 40-year-old male patient with DM who presented with acute kidney injury, and was initially pulsed with methylprednisolone for 3 days, followed by dexamethasone equivalent to 1 mg/kg/day prednisolone. He was subsequently found to have SAGN on kidney biopsy along with staphylococcus bacteraemia and left knee septic arthritis. With proof of definitive infection, intravenous immunoglobulin 2 g/kg over 2 days was given and steroids were reduced. He was treated with intravenous vancomycin. With treatment, the general condition of the patient improved. On day 38, he developed infective endocarditis and died of congestive heart failure subsequently. Undiagnosed staphylococcal sepsis complicating a rheumatological disease course can lead to complications like SAGN, infective endocarditis and contribute to increased morbidity and mortality, as is exemplified by our case.
Acute lead poisoning: a diagnostic challenge in the emergency department
Authors: Gopinath Bharath , Kappagantu Vignan , Mathew Roshan , Jamshed Nayer
Published: January 2021

Acute abdominal pain is a common presentation to the emergency department (ED). Ruling out life-threatening causes and giving pain relief are the most important tasks in ED. We describe a 32-year-old man who presented to ED with abdominal pain and vomiting which was unrelieved by usual doses of analgesic. Extensive investigations revealed no significant abnormalities. On further probing, he admitted taking traditional medications for infertility. The toxicological panel revealed a high blood lead level, leading to a diagnosis of acute lead toxicity. Chelation therapy with D-penicillamine was initiated and the patient’s abdominal pain resolved within 4 days.
Home and Online Management and Evaluation of Blood Pressure (HOME BP) using a digital intervention in poorly controlled hypertension: randomised controlled trial
Authors: McManus Richard J , Little Paul , Stuart Beth , Morton Katherine , Raftery James , Kelly Jo , Bradbury Katherine , Zhang Jin , Zhu Shihua , Murray Elizabeth , May Carl R , Mair Frances S , Michie Susan , Smith Peter , Band Rebecca , Ogburn Emma , Allen Julie , Rice Cathy , Nuttall Jacqui , Williams Bryan , Yardley Lucy
Published: January 2021

Objective

The HOME BP (Home and Online Management and Evaluation of Blood Pressure) trial aimed to test a digital intervention for hypertension management in primary care by combining self-monitoring of blood pressure with guided self-management.

Design

Unmasked randomised controlled trial with automated ascertainment of primary endpoint.

Setting

76 general practices in the United Kingdom.

Participants

622 people with treated but poorly controlled hypertension (>140/90 mm Hg) and access to the internet.

Interventions

Participants were randomised by using a minimisation algorithm to self-monitoring of blood pressure with a digital intervention (305 participants) or usual care (routine hypertension care, with appointments and drug changes made at the discretion of the general practitioner; 317 participants). The digital intervention provided feedback of blood pressure results to patients and professionals with optional lifestyle advice and motivational support. Target blood pressure for hypertension, diabetes, and people aged 80 or older followed UK national guidelines.

Main outcome measures

The primary outcome was the difference in systolic blood pressure (mean of second and third readings) after one year, adjusted for baseline blood pressure, blood pressure target, age, and practice, with multiple imputation for missing values.

Results

After one year, data were available from 552 participants (88.6%) with imputation for the remaining 70 participants (11.4%). Mean blood pressure dropped from 151.7/86.4 to 138.4/80.2 mm Hg in the intervention group and from 151.6/85.3 to 141.8/79.8 mm Hg in the usual care group, giving a mean difference in systolic blood pressure of −3.4 mm Hg (95% confidence interval −6.1 to −0.8 mm Hg) and a mean difference in diastolic blood pressure of −0.5 mm Hg (−1.9 to 0.9 mm Hg). Results were comparable in the complete case analysis and adverse effects were similar between groups. Within trial costs showed an incremental cost effectiveness ratio of £11 ($15, €12; 95% confidence interval £6 to £29) per mm Hg reduction.

Conclusions

The HOME BP digital intervention for the management of hypertension by using self-monitored blood pressure led to better control of systolic blood pressure after one year than usual care, with low incremental costs. Implementation in primary care will require integration into clinical workflows and consideration of people who are digitally excluded.

Trial registration

ISRCTN13790648
.
Impact of military medicine on civilian medical practice in the UK from 2009 to 2020
Authors: France Katherine , Handford C
Published: January 2021

Introduction

The positive impact of advances in military medicine and the influence these have had on civilian medical practice have been well documented throughout history: this review will be looking specifically between 2009 and 2020.

Aims

Review of innovations that have been implemented or have influenced civilian practice within the areas of trauma, disease outbreak management and civilian systems between 2009 and 2020. This review will also aim to explore the impact that working with or within the military can have on individuals within civilian healthcare systems and the future challenges we face to maintain skills.

Results

Using a narrative approach to this review, we found that there have been numerous changes to trauma management within the UK, based on military practice and research during conflict, which have improved survival outcomes. In addition, the use of niche military skills as part of a coordinated response, during both internal and international disease outbreaks, are thought to have supported civilian systems enabling an efficient and prolonged response. Furthermore, adaptation of military concepts and their application to the NHS through consultant-led prehospital teams, centralisation of specialties in the form of major trauma centres and the introduction of guidelines to manage 'major incidents and mass casualty events' in 2018 have improved patient outcomes.

Conclusion

From 2009 to 2020, lessons learnt from the British and other nations’ militaries have been integrated into UK practice and have likely contributed to improved outcomes in the management of major incidents both nationally and internationally.
Impaired antibacterial response of liver sinusoidal Vγ9+Vδ2+ T cells in patients with chronic liver disease
Authors: Rha Min-Seok , Han Ji Won , Koh June-Young , Lee Ha Seok , Kim Jong Hoon , Cho Kyungjoo , Kim Soon Il , Kim Myoung Soo , Lee Jae Geun , Park Su-Hyung , Joo Dong Jin , Park Jun Yong , Shin Eui-Cheol
Published: January 2021

Objective

The liver acts as a frontline barrier against diverse gut-derived pathogens, and the sinusoid is the primary site of liver immune surveillance. However, little is known about liver sinusoidal immune cells in the context of chronic liver disease (CLD). Here, we investigated the antibacterial capacity of liver sinusoidal γδ T cells in patients with various CLDs.

Design

We analysed the frequency, phenotype and functions of human liver sinusoidal γδ T cells from healthy donors and recipients with CLD, including HBV-related CLD (liver cirrhosis (LC) and/or hepatocellular carcinoma (HCC)), alcoholic LC and LC or HCC of other aetiologies, by flow cytometry and RNA-sequencing using liver perfusates obtained during living donor liver transplantation. We also measured the plasma levels of D-lactate and bacterial endotoxin to evaluate bacterial translocation.

Results

The frequency of liver sinusoidal Vγ9+Vδ2+ T cells was reduced in patients with CLD. Immunophenotypic and transcriptomic analyses revealed that liver sinusoidal Vγ9+Vδ2+ T cells from patients with CLD were persistently activated and pro-apoptotic. In addition, liver sinusoidal Vγ9+Vδ2+ T cells from patients with CLD showed significantly decreased interferon (IFN)-γ production following stimulation with bacterial metabolites and Escherichia coli. The antibacterial IFN-γ response of liver sinusoidal Vγ9+Vδ2+ T cells significantly correlated with liver function, and inversely correlated with the plasma level of D-lactate in patients with CLD. Repetitive in vitro stimulation with E. coli induced activation, apoptosis and functional impairment of liver sinusoidal Vγ9+Vδ2+ T cells.

Conclusion

Liver sinusoidal Vγ9+Vδ2+ T cells are functionally impaired in patients with CLD. Bacterial translocation and decreasing liver functions are associated with functional impairment of liver sinusoidal Vγ9+Vδ2+ T cells.
Information entropy evaluation model of bus-line reliability considering the combination of bus stops and bus travel time
Authors: Lai Yuanwen , Ma Zhenhong , Xu Shutian , Easa Said M.
Published: January 2021

Evaluating the reliability of a bus line can provide useful information on the service performance of the city’s bus transit system and the need for improvements. This paper presents a reliability evaluation model of a bus line based on information entropy. The model integrates the weighted bus-stop index and the variation index of bus travel time. To better determine the weights of the bus stop, six indices were established based on three characteristics: passenger flow, bus-stop properties, and the environment. The proposed model was applied to typical bus lines in Fuzhou, People’s Republic of China. The results show that most bus-stop reliabilities at the peak period were smaller than those at the off-peak period. In addition, for either peak or off-peak period, the reliability shows a slight upward trend following a gradual decline after the first stop, generally reflecting the influence of passenger flow, environment, and location factors.
Comparative genomics of the Pasteurella multocida toxin
Authors: Siddaramappa Shivakumara
Published: January 2021

Pasteurella multocida is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups (A, B, D, E, and F) and 16 serotypes of P. multocida have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by P. multocida strains containing toxA, which encodes a 146 kDa heat-labile toxin. Among the five serogroups, only some strains of serogroups A and D are toxigenic. In this study, by comparative analyses of the genomes of many strains, it has been shown that toxA is sparsely distributed in P. multocida. Furthermore, full-length homologs of P. multocida toxA were found only in two other bacterial species. It has also been shown that toxA is usually associated with a prophage, and that some strains contain an orthologous prophage but not toxA. Among the toxA-containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among P. multocida strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group P. multocida strains in relation to their serotypes and (or) genotypes. It remains to be determined if the toxA-containing prophages in strains HN01 and HN06 are inducible, and if they can be used for lysogenic transfer of toxA to other bacteria.
Some Theorems on Leibniz n-Algebras from the Category Un (Lb)
Authors: Kim Min Soo , Turdibaev Rustam
Published: January 2021

We study the Leibniz [Formula: see text]-algebra [Formula: see text], whose multiplication is defined via the bracket of a Leibniz algebra [Formula: see text] as [Formula: see text]. We show that [Formula: see text] is simple if and only if [Formula: see text] is a simple Lie algebra. An analog of Levi's theorem for Leibniz algebras in [Formula: see text] is established and it is proven that the Leibniz [Formula: see text]-kernel of [Formula: see text] for any semisimple Leibniz algebra [Formula: see text] is the [Formula: see text]-algebra [Formula: see text].
Experiment Improvement of Restricted Boltzmann Machine Methods for Image Classification
Authors: Dewi Christine , Chen Rung-Ching , Hendry  , Hung Hsiu-Te
Published: January 2021

Restricted Boltzmann machine (RBM) plays an important role in current deep learning techniques, as most of the existing deep networks are based on or related to generative models and image classification. Many applications for RBMs have been developed for a large variety of learning problems. Recent developments have demonstrated the capacity of RBM to be powerful generative models, able to extract useful features from input data or construct deep artificial neural networks. In this work, we propose a learning algorithm to find the optimal model complexity for the RBM by improving the hidden layer (50–750 layers). Then, we compare and analyze the classification performance in depth of regular RBM use RBM () function, classification RBM use stackRBM() function, and Deep Belief Network (DBN) use DBN() function with the different hidden layer. As a result, Stacking RBM and DBN could improve our classification performance compared to regular RBM.
A Relational-Database Methodology for Incorporating Consciousness into AI Agents
Authors: Wolfson Ouri
Published: January 2021

Consciousness is key to Artificial General Intelligence. It is currently unclear what is consciousness and we expect that by the time it is understood, there will probably be millions of man-years invested in the development of AI agents. This paper addresses the following question. How should AI agents be engineered from now on, such that when it becomes clear how consciousness and subjective experiences are generated, the effort of endowing AI agents and robots existing at that time with consciousness is minimized. As far as we know this question has not been studied heretofore. The paper proposes a methodology and architecture that are based on evolving Probabilistic Relational Databases, and on stepwise progressive data fusion. The methodology and architecture are independent of what consciousness turns out to be, provided that it can be incorporated into AI agents.
Microbial and thermochemical controlled sulfur cycle in the Early Triassic sediments of the Western Canadian Sedimentary Basin
Authors: Liseroudi Mastaneh H. , Ardakani Omid H. , Pedersen Per K. , Stern Richard A. , Wood James M. , Sanei Hamed
Published: January 2021

Pyrite is one of three main sulfur reservoirs and one of the biggest fluxes in the global sulfur cycle. The sulfur isotopic signature of hydrogen sulfide, pyrite and their parent sulfate is widely used as a proxy for tracking sulfur cycle variations in diagenetic environments. The Early Triassic Montney Formation in the Western Canadian Sedimentary Basin is characterized by distinct regional variations in pyrite abundance, type, sulfur isotopic signature and H
2
S concentrations in natural gas. Two main types of framboidal and crystalline pyrite were identified to have formed during various stages of diagenesis. The wide range of δ
34
S
pyrite
values (−34.4 to  + 57.8‰ V-CDT) demonstrates that the sulfur cycle in the Montney Formation is governed by both microbial and thermochemical processes. The comparison of δ
34
S of the produced-gas H
2
S with pyrite, anhydrite and solid bitumen of the Montney, and underlying and overlying formations, suggests a mixture of dominantly
in situ
and minor migrated H
2
S with thermochemical sulfate reduction origin in the Montney Formation. The large diagenetic variations in pyrite types and δ
34
S
pyrite
values suggest a lack of direct biogeochemical connection to the sulfur cycle and emphasize the importance of careful petrographic observations and micro-scale isotopic analysis of sedimentary units to accurately reconstruct paleoenvironmental conditions.

Supplementary material:
Methodology and δ
34
S results are available at
https://doi.org/10.6084/m9.figshare.c.5272484
Chapter 2.2a Palmer Land and Graham Land volcanic groups (Antarctic Peninsula): volcanology
Authors: Riley Teal R. , Leat Philip T.
Published: January 2021

The break-up of Gondwana during the Early–Middle Jurassic was associated with flood basalt volcanism in southern Africa and Antarctica (Karoo–Ferrar provinces), and formed one of the most extensive episodes of continental magmatism of the Phanerozoic. Contemporaneous felsic magmatism along the proto-Pacific margin of Gondwana has been referred to as a silicic large igneous province, and is exposed extensively in Patagonian South America, the Antarctic Peninsula and elsewhere in West Antarctica. Jurassic-age silicic volcanism in Patagonia is defined as the Chon Aike province and forms one of the most voluminous silicic provinces globally. The Chon Aike province is predominantly pyroclastic in origin, and is characterized by crystal tuffs and ignimbrite units of rhyolite composition. Silicic volcanic rocks of the once contiguous Antarctic Peninsula form a southward extension of the Chon Aike province and are also dominated by silicic ignimbrite units, with a total thickness exceeding 1 km. The ignimbrites include high-grade rheomorphic ignimbrites, as well as unwelded, lithic-rich ignimbrites. Rhyolite lava flows, air-fall horizons, debris-flow deposits and epiclastic deposits are volumetrically minor, occurring as interbedded units within the ignimbrite succession.
Chapter 1.2 Antarctic volcanism: volcanology and palaeoenvironmental overview
Authors: Smellie John L.
Published: January 2021

Since Jurassic time (
c.
200 Ma), Antarctica has had a greater diversity of volcanism than other southern continents. It includes: (1) voluminous mafic and felsic volcanism associated with the break-up of Gondwana; (2) a long-lived continental margin volcanic arc, including back-arc alkaline volcanism linked to slab rollback; (3) small-volume mafic alkaline volcanism associated with slab-window formation; and (4) one of Earth's major continental rift zones, the West Antarctic Rift System (WARS), with its numerous large alkaline central volcanoes. Several of Antarctica's volcanoes are still active. This chapter is a review of the major volcanic episodes and their principal characteristics, in their tectonic, volcanological and palaeoenvironmental contexts. Jurassic Gondwana break-up was associated with large-scale volcanism that caused global environmental changes and associated mass extinctions. The volcanic arc was a major extensional arc characterized by alternating volcanic flare-ups and lulls. The Neogene rift-related alkaline volcanism is dominated by effusive glaciovolcanic eruptions, overwhelmingly as both pāhoehoe- and ‘a‘ā-sourced lava-fed deltas. The rift is conspicuously poor in pyroclastic rocks due to the advection and removal of tephra erupted during glacial intervals. Volcanological investigations of the Neogene volcanism have also significantly increased our knowledge of the critical parameters and development of the Antarctic Ice Sheet.
Chapter 1.3 Antarctic volcanism: petrology and tectonomagmatic overview
Authors: Panter Kurt Samuel
Published: January 2021

Petrological investigations over the past 30 years have significantly advanced our knowledge of the origin and evolution of magmas emplaced within and erupted on top of the Antarctic Plate. Over the last 200 myr Antarctica has experienced: (1) several episodes of rifting, leading to the fragmentation of Gondwana and the formation by
c.
83 Ma of the current Antarctica Plate; (2) long-lived subduction that shut down progressively eastwards along the Gondwana margin in the Late Cretaceous and is still active at the northernmost tip of the Antarctic Peninsula; and (3) broad extension across West Antarctica that produced one of the Earth's major continental rift systems. The dynamic tectonic history of Antarctica since the Triassic has led to a diversity of volcano types and igneous rock compositions with correspondingly diverse origins. Many intriguing questions remain about the petrology of mantle sources and the mechanisms for melting during each tectonomagmatic phase. For intraplate magmatism, the upwelling of deep mantle plumes is often evoked. Alternatively, subduction-related metasomatized mantle sources and melting by more passive means (e.g. edge-driven flow, translithospheric faulting, slab windows) are proposed. A brief review of these often competing models is provided in this chapter along with recommendations for ongoing petrological research in Antarctica.
Chapter 1.4 Antarctic volcanism: active volcanism overview
Authors: Geyer A.
Published: January 2021

In the last two centuries, demographic expansion and extensive urbanization of volcanic areas have increased the exposure of our society to volcanic hazards. Antarctica is no exception. During the last decades, the permanent settlement and seasonal presence of scientists, technicians, tourists and logistical personnel close to active volcanoes in the south polar region have increased notably. This has led to an escalation in the number of people and the amount of infrastructure exposed to potential eruptions. This requires advancement of our knowledge of the volcanic and magmatic history of Antarctic active volcanoes, significant improvement of the monitoring networks, and development of long-term hazard assessments and vulnerability analyses to carry out the required mitigation actions, and to elaborate on the most appropriate response plans to reduce loss of life and infrastructure during a future volcanic crisis. This chapter provides a brief summary of the active volcanic systems in Antarctica, highlighting their main volcanological features, which monitoring systems are deployed (if any), and recent (i.e. Holocene and/or historical) eruptive activity or unrest episodes. To conclude, some notes about the volcanic hazard assessments carried out so far on south polar volcanoes are also included, along with recommendations for specific actions and ongoing research on active Antarctic volcanism.
StreamGen
Authors: Guerriero Michele , Tamburri Damian Andrew , Nitto Elisabetta Di
Published: January 2021

Distributed streaming applications, i.e., applications that process massive streams of data in a distributed fashion, are becoming increasingly popular to tame the velocity and the volume of
Big Data
. Nevertheless, the widespread adoption of data-intensive processing is still limited by the non-trivial design paradigms involved, which deal with the unboundedness and volume of involved data streams and by the many distributed streaming platforms, each with its own characteristics and APIs. In this article, we present StreamGen, a Model-Driven Engineering tool to simplify the design of such streaming applications and automatically generate the corresponding code. StreamGen is able to automatically generate fully working and processing-ready code for different target platforms (e.g., Apache Spark, Apache Flink). Evaluation shows that (i) StreamGen is general enough to model and generate the code, offering comparable performance against a preexisting similar and well-known application; (ii) the tool is fully compliant with streaming concepts defined as part of the Google Dataflow Model; and (iii) users with little computer science background and limited experience with big data have been able to work with StreamGen and create/refactor an application in a matter of minutes.
Verification of Program Transformations with Inductive Refinement Types
Authors: Al-Sibahi Ahmad Salim , Jensen Thomas P. , Dimovski Aleksandar S. , Wąsowski Andrzej
Published: January 2021

High-level transformation languages like Rascal include expressive features for manipulating large abstract syntax trees: first-class traversals, expressive pattern matching, backtracking, and generalized iterators. We present the design and implementation of an abstract interpretation tool, Rabit, for verifying inductive type and shape properties for transformations written in such languages. We describe how to perform abstract interpretation based on operational semantics, specifically focusing on the challenges arising when analyzing the expressive traversals and pattern matching. Finally, we evaluate Rabit on a series of transformations (normalization, desugaring, refactoring, code generators, type inference, etc.) showing that we can effectively verify stated properties.
Machete
Authors: Taranta II Eugene M. , Pittman Corey R. , Maghoumi Mehran , Maslych Mykola , Moolenaar Yasmine M. , Laviola Jr Joseph J.
Published: January 2021

We present Machete, a straightforward segmenter one can use to isolate custom gestures in continuous input. Machete uses traditional continuous dynamic programming with a novel dissimilarity measure to align incoming data with gesture class templates in real time. Advantages of Machete over alternative techniques is that our segmenter is computationally efficient, accurate, device-agnostic, and works with a single training sample. We demonstrate Machete’s effectiveness through an extensive evaluation using four new high-activity datasets that combine puppeteering, direct manipulation, and gestures. We find that Machete outperforms three alternative techniques in segmentation accuracy and latency, making Machete the most performant segmenter. We further show that when combined with a custom gesture recognizer, Machete is the only option that achieves both high recognition accuracy and low latency in a video game application.
Fast and Secure Authentication in Virtual Reality Using Coordinated 3D Manipulation and Pointing
Authors: Mathis Florian , Williamson John H. , Vaniea Kami , Khamis Mohamed
Published: January 2021

There is a growing need for usable and secure authentication in immersive virtual reality (VR). Established concepts (e.g., 2D authentication schemes) are vulnerable to observation attacks, and most alternatives are relatively slow. We present RubikAuth, an authentication scheme for VR where users authenticate quickly and secure by selecting digits from a virtual 3D cube that leverages coordinated 3D manipulation and pointing. We report on results from three studies comparing how pointing using eye gaze, head pose, and controller tapping impact RubikAuth’s usability, memorability, and observation resistance under three realistic threat models. We found that entering a four-symbol RubikAuth password is fast: 1.69–3.5 s using controller tapping, 2.35–4.68 s using head pose and 2.39 –4.92 s using eye gaze, and highly resilient to observations: 96–99.55% of observation attacks were unsuccessful. RubikAuth also has a large theoretical password space: 45

n

for an
n
-symbols password. Our work underlines the importance of considering novel but realistic threat models beyond standard one-time attacks to fully assess the observation-resistance of authentication schemes. We conclude with an in-depth discussion of authentication systems for VR and outline five learned lessons for designing and evaluating authentication schemes.
The Nudge Puzzle
Authors: Zimmermann Verena , Renaud Karen
Published: January 2021

Nudging is a promising approach, in terms of influencing people to make advisable choices in a range of domains, including cybersecurity. However, the processes underlying the concept and the nudge’s effectiveness in different contexts, and in the long term, are still poorly understood. Our research thus first reviewed the nudge concept and differentiated it from other interventions before applying it to the cybersecurity area. We then carried out an empirical study to assess the effectiveness of three different nudge-related interventions on four types of cybersecurity-specific decisions. Our study demonstrated that the combination of a simple nudge and information provision, termed a “hybrid nudge,” was at least as, and in some decision contexts even more effective in encouraging secure choices as the simple nudge on its own. This indicates that the inclusion of information when deploying a nudge, thereby increasing the intervention’s transparency, does not necessarily diminish its effectiveness.

A follow-up study explored the educational and long-term impact of our tested nudge interventions to encourage secure choices. The results indicate that the impact of the initial nudges, of all kinds, did not endure. We conclude by discussing our findings and their implications for research and practice.
Best Practice: Application Frameworks
Authors: Nokleberg Chris , Hawkes Brad
Published: January 2021

While frameworks can be a powerful tool, they have some disadvantages and may not make sense for all organizations. Framework maintainers need to provide standardization and well-defined behavior while not being overly prescriptive. When frameworks strike the right balance, however, they can offer large developer productivity gains. The consistency provided by widespread use of frameworks is a boon for other teams such as SRE and security that have a vested interest in the quality of applications. Additionally, the structure of frameworks provides a foundation for building higher-level abstractions such as microservices platforms, which unlock new opportunities for system architecture and automation. At Google, such frameworks and platforms have seen broad organic adoption and have had a significant positive impact.
Glucosinolates in Brassica Vegetables: Characterization and Factors That Influence Distribution, Content, and Intake
Authors: Wu Xianli , Huang Hui , Childs Holly , Wu Yanbei , Yu Liangli , Pehrsson Pamela R.
Published: January 2021

Glucosinolates (GSLs) are a class of sulfur-containing compounds found predominantly in the genus Brassica of the Brassicaceae family. Certain edible plants in Brassica, known as Brassica vegetables, are among the most commonly consumed vegetables in the world. Over the last three decades, mounting evidence has suggested an inverse association between consumption of Brassica vegetables and the risk of various types of cancer. The biological activities of Brassica vegetables have been largely attributed to the hydrolytic products of GSLs. GSLs can be hydrolyzed by enzymes; thermal or chemical degradation also breaks down GSLs. There is considerable variation of GSLs in Brassica spp., which are caused by genetic and environmental factors. Most Brassica vegetables are consumed after cooking; common cooking methods have a complex influence on the levels of GSLs. The variationof GSLs in Brassica vegetables and the influence of cooking and processing methods ultimately affect their intake and health-promoting properties.
Study of a Fringing Field Biosensor Tunnel-FET
Authors: Macambira C. N. , Agopian P. G. D. , Martino J. A.
Published: January 2021

In this paper, we present a comprehensive study of the Fringing Field Biosensor Tunnel-FET (Bio-TFET) device based on 2D-device simulation. The presence of a biomaterial with a distinct dielectric constant (k, where ε = k*ε
0) on the underlap region (LUD) between gate and drain affects the ambipolar drain current (ID). The Bio-TFET can be observed in the ambipolar region (i.e., for negative gate voltage in an n type Bio-nTFET device) due to the variation of the k, biomaterial thicknesses (tBio), the LUD, and/or the presence of charges (QBio) into the biomaterial/silicon interface. The results show that the maximum sensitivity is observed when LUD = 30 nm (3 orders of magnitude higher compared with LUD of 25 nm lower or higher than 30 nm). When tBio increases from 10 nm to 30 nm (for k = 10), the sensitivity increases up to 1 orders of magnitude. The presence of QBio into the biomaterial also increases the sensitivity of 60 times for a fixed value of tBio = 30 nm and k = 10 and QBio changing from 1 × 1010 cm−2 to 1 × 1012 cm−2. The results show that the sensitivity of the fringing field Bio-nTFET is strongly dependent on the tunneling length modulation.
Wet Alkaline Etching of Si Selectively to SiGe for sub 10 nm Gate All Around Architectures
Authors: Rachidi Sana , Loup Virginie , Campo Alain , Hartmann Jean-Michel , Posseme Nicolas
Published: January 2021

Using alkaline chemistries for SiGe based Gate-All-Around architectures fabrication is still a challenge. This work reports a detailed study of Si to Si0.7Ge0.3 selective etching using NH4OH, TMAH and TEAH alkaline etchants. These alkaline solutions have all shown a great selectivity with respect to SiGe (up to 300). X-ray Photoelectron Spectroscopy and Atomic Force Microscopy have evidenced the presence of a smooth mix of SiOx + GeOx oxides during SiGe alkaline etching, which explains the obtained selectivity. When such alkaline etching processes were used on wafers with mesas etched in [Si 8 nm/Si0.7Ge0.3 8 nm] × 2 superlattices, an anisotropic behavior toward Si (111) was noticed with Scanning Electron Microscopy. Only 6 nm (or <6 nm) wide devices could be fabricated with the studied alkaline chemistries. Releasing wider SiGe nanowires required greater Si sacrificial layers’ thicknesses than √2 Critical Dimension. Finally, addition of peroxide to NH4OH alkaline chemistry reduced NH4OH anisotropy with respect to Si (111) planes, enabling the release of 10 nm wide SiGe nanowires without increasing the thickness of Si sacrificial layers.
Highly Ordered Alumina Through-Hole Membranes Having Reduced Hole Intervals: 30–50 nm
Authors: Yanagishita Takashi , Kato Atsushi , Nakamura Takaki , Masuda Hideki
Published: January 2021

We investigated the dependence of the solubility of the oxide layer formed by anodization of Al on the concentration of sulfuric acid. As a result, it was found that the solubility of anodic porous alumina formed in sulfuric acid electrolyte could be controlled by adjusting the concentration of sulfuric acid. On the basis of these results, highly ordered alumina through-hole membranes with reduced hole intervals, 30–50 nm, were formed by two-layer anodization, where one of the oxide layers was selectively dissolved in accordance with the concentration of sulfuric acid used for anodization in the postetching treatment. The obtained ordered alumina through-hole membranes with reduced hole intervals are expected to be applied to various functional devices requiring a highly ordered through-hole array of reduced size.
Influence of Zr on Thermal Stability and Microstructure of Sb2Te Film
Authors: Tao Ying , Zhang Yu , Ma Yadong , You Zhenzhen , Lu Yegang
Published: January 2021

The influence of Zr on crystallization behavior of Sb2Te films were investigated systematically. With the increase of Zr from 0 to 8 at.%, the crystalline temperature of Zr-Sb2Te improves from 140 oC to 210 oC, and the data retention maintaining for 10 year significantly increases from 48.9 oC to 115.1 oC. All of the crystalline Zr-Sb2Te films retain the stable phase of Sb2Te without phase separation, which has advantages in endurance of the phase change device. The Zr atoms form chemical bonds with Sb and Te, which leads to the improvement in thermal stability of the amorphous Sb2Te. The grain size is significantly refined by Zr doping, which results in the increasement of the crystalline resistivity. These results could pave the way for Zr-Sb-Te to developing the nonvolatile and reconfigurable devices.
Role of platelets in regulating activated coagulation factor XI activity
Authors: Reitsma Stéphanie E. , Pang Jiaqing , Raghunathan Vikram , Shatzel Joseph J. , Lorentz Christina U. , Tucker Erik I. , Gruber András , Gailani David , McCarty Owen J. T. , Puy Cristina
Published: January 2021

Factor XI (FXI) has been shown to bind platelets, but the functional significance of this observation remains unknown. Platelets are essential for hemostasis and play a critical role in thrombosis, whereas FXI is not essential for hemostasis but promotes thrombosis. An apparent functional contradiction, platelets are known to support thrombin generation, yet platelet granules release protease inhibitors, including those of activated FXI (FXIa). We aim to investigate the secretory and binding mechanisms by which platelets could support or inhibit FXIa activity. The presence of platelets enhanced FXIa activity in a purified system and increased coagulation Factor IX (FIX) activation by FXIa and fibrin generation in human plasma. In contrast, platelets reduced the activation of FXI by activated coagulation factor XII (FXIIa) and the activation of FXII by kallikrein (PKa). Incubation of FXIa with the platelet secretome, which contains FXIa inhibitors, such as protease nexin-II, abolished FXIa activity, yet in the presence of activated platelets, the secretome was not able to block the activity of FXIa. FXIa variants lacking the anion-binding sites did not alter the effect of platelets on FXIa activity or interaction. Western blot analysis of bound FXIa [by FXIa-platelet membrane immunoprecipitation] showed that the interaction with platelets is zinc dependent and, unlike FXI binding to platelets, not dependent on glycoprotein Ib. FXIa binding to the platelet membrane increases its capacity to activate FIX in plasma likely by protecting it from inhibition by inhibitors secreted by activated platelets. Our findings suggest that an interaction of FXIa with the platelet surface may induce an allosteric modulation of FXIa.
GCSF deficiency attenuates nonalcoholic fatty liver disease through regulating GCSFR-SOCS3-JAK-STAT3 pathway and immune cells infiltration
Authors: Zhang Yuwei , Zhou Xuefeng , Liu Peihao , Chen Xueyang , Zhang Jie , Zhang Hong , Li Sha , Chen Yishu , Song Xin , Wang Jinghua , Zeng Hang , Zhang Xiaofen , Tang Chenxi , Yu Chaohui , Li Youming , Xu Chengfu
Published: January 2021

We found GCSF was involved in lipid metabolism and NAFLD development. GCSF administration increased serum triglyceride levels in patients. GCSF deficiency alleviated HFD-induced insulin resistance and hepatic steatosis in mice. GCSF could directly act on hepatocytes through GCSFR-SOCS3-JAK-STAT3 pathway, and regulate the infiltration of immune cells into the liver to indirectly modulate NAFLD. Our finding indicates that GCSF may provide new strategies for the treatment of NAFLD.
Bacterial and eukaryotic extracellular vesicles and nonalcoholic fatty liver disease: new players in the gut-liver axis?
Authors: Villard Alexandre , Boursier Jérôme , Andriantsitohaina Ramaroson
Published: January 2021

The liver and intestine communicate in a bidirectional way through the biliary tract, portal vein, and other components of the gut-liver axis. The gut microbiota is one of the major contributors to the production of several proteins and bile acids. Imbalance in the gut bacterial community, called dysbiosis, participates in the development and progression of several chronic liver diseases, such as nonalcoholic fatty liver disease (NAFLD). NAFLD is currently considered the main chronic liver disease worldwide. Dysbiosis contributes to NAFLD development and progression, notably by a greater translocation of pathogen-associated molecular patterns (PAMPs) in the blood. Lipopolysaccharide (LPS) is a PAMP that activates Toll-like receptor 4 (TLR4), induces liver inflammation, and participates in the development of fibrogenesis. LPS can be transported by bacterial extracellular vesicles (EVs). EVs are spherical structures produced by eukaryotic and prokaryotic cells that transfer information to distant cells and may represent new players in NAFLD development and progression. The present review summarizes the role of eukaryotic EVs, either circulating or tissue-derived, in NAFLD features, such as liver inflammation, angiogenesis, and fibrosis. Circulating EV levels are dynamic and correlate with disease stage and severity. However, scarce information is available concerning the involvement of bacterial EVs in liver disease. The present review highlights a potential role of bacterial EVs in insulin resistance and liver inflammation, although the mechanism involved has not been elucidated. In addition, because of their distinct signatures, eukaryotic and prokaryotic EVs may also represent a promising NAFLD diagnostic tool as a “liquid biopsy” in the future.
Stomach region stimulated determines effects on duodenal motility in rats
Authors: Tan Zhenjun T. , Ward Matthew , Phillips Robert J. , Zhang Xueguo , Jaffey Deborah M. , Chesney Logan , Rajwa Bartek , Baronowsky Elizabeth A. , McAdams Jennifer , Powley Terry L.
Published: January 2021

Gastric electrical stimulation (GES) is used clinically to promote proximal GI emptying and motility. In acute experiments, we measured duodenal motor responses elicited by GES applied at 141 randomly chosen electrode sites on the stomach serosal surface. Overnight-fasted (H2O available) anesthetized male rats ( n = 81) received intermittent biphasic GES for 5 min (20-s-on/40-s-off cycles; I = 0.3 mA; pw = 0.2 ms; 10 Hz). A strain gauge on the serosal surface of the proximal duodenum of each animal was used to evaluate baseline motor activity and the effect of GES. Using ratios of time blocks compared with a 15-min prestimulation baseline, we evaluated the effects of the 5-min stimulation on concurrent activity, on the 10 min immediately after the stimulation, and on the 15-min period beginning with the onset of stimulation. We mapped the magnitude of the duodenal response (three different motility indices) elicited from the 141 stomach sites. Post hoc electrode site maps associated with duodenal responses suggested three zones similar to the classic regions of forestomach, corpus, and antrum. Maximal excitatory duodenal motor responses were elicited from forestomach sites, whereas inhibitory responses occurred with stimulation of the corpus. Moderate excitatory duodenal responses occurred with stimulation of the antrum. Complex, weak inhibitory/excitatory responses were produced by stimulation at boundaries between stomach regions. Patterns of GES efficacies coincided with distributions of previously mapped vagal afferents, suggesting that excitation of the duodenum is strongest when GES electrodes are situated over stomach concentrations of vagal intramuscular arrays, putative stretch receptors in the muscle wall.