bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxygen and nitrogen production by an ammonia-oxidizing archaeon
Authors: Kraft Beate , Jehmlich Nico , Larsen Morten , Bristow Laura A. , Könneke Martin , Thamdrup Bo , Canfield Donald E.
Published: January 2022

Consuming oxygen, but making it too

For marine microbes, there are myriad biological reactions involved in the cycling of nutrients and the generation of energy. Availability of oxygen is crucial for many species’ metabolism. Kraft
et al
. were surprised to find that pure cultures of an ammonia-oxidizing archaean (AOA) (see the Perspective by Martens-Habbena and Qin),
Nitosopumilus maritimus
, were able to regenerate small amounts of oxygen when placed under anoxic conditions. Isotope labeling of nitrogen species revealed a series of reactions transforming nitrite, the expected metabolic end product, into nitric oxide, nitrous oxide, and, eventually, dinitrogen. Oxygen was also formed, likely from nitric oxide disproportionation, but was mostly consumed, which is consistent with the overall aerobic metabolism of AOA. These organisms can be found in oxygen-depleted waters and may benefit from producing oxygen from nitrite under these conditions. —MAF
Cryo-EM structure of human GPR158 receptor coupled to the RGS7-Gβ5 signaling complex
Authors: Patil Dipak N. , Singh Shikha , Laboute Thibaut , Strutzenberg Timothy S. , Qiu Xingyu , Wu Di , Novick Scott J. , Robinson Carol V. , Griffin Patrick R. , Hunt John F. , Izard Tina , Singh Appu K. , Martemyanov Kirill A.
Published: January 2022

Not your typical GPCR

Among the large family of G protein–coupled receptors (GPCRs) are many orphans, so called because their signaling reactions remain poorly understood. Among these is GPR158 which is highly expressed in the nervous system and implicated in processes from cognition to memory to mood. Patil
et al
. determined a high-resolution structure of GPR158 alone and bound to a regulator of G protein signaling (RGS) complex. GPR158 has an unusual dimerization mode with an extensive interaction interface that locks it in a conformation that likely prevents G protein activation. RGS binds to the homodimer at a site that substantially overlaps the surface that binds G proteins, again preventing canonical G protein signaling. Binding of a ligand to the extracellular domain may regulate signaling through the RGS complex. —VV
Immune correlates analysis of the mRNA-1273 COVID-19 vaccine efficacy clinical trial
Authors: Gilbert Peter B. , Montefiori David C. , McDermott Adrian B. , Fong Youyi , Benkeser David , Deng Weiping , Zhou Honghong , Houchens Christopher R. , Martins Karen , Jayashankar Lakshmi , Castellino Flora , Flach Britta , Lin Bob C. , O’Connell Sarah , McDanal Charlene , Eaton Amanda , Sarzotti-Kelsoe Marcella , Lu Yiwen , Yu Chenchen , Borate Bhavesh , van der Laan Lars W. P. , Hejazi Nima S. , Huynh Chuong , Miller Jacqueline , El Sahly Hana M. , Baden Lindsey R. , Baron Mira , De La Cruz Luis , Gay Cynthia , Kalams Spyros , Kelley Colleen F. , Andrasik Michele P. , Kublin James G. , Corey Lawrence , Neuzil Kathleen M. , Carpp Lindsay N. , Pajon Rolando , Follmann Dean , Donis Ruben O. , Koup Richard A. ,   Immune Assays Team§,   Moderna, Inc. Team§,   Coronavirus Vaccine Prevention Network (CoVPN)/Coronavirus Efficacy (COVE) Team§,   United States Government (USG)/CoVPN Biostatistics Team§
Published: January 2022

Antibody levels predict vaccine efficacy

Symptomatic COVID-19 infection can be prevented by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines. A “correlate of protection” is a molecular biomarker to measure how much immunity is needed to fight infection and is key for successful global immunization programs. Gilbert
et al
. determined that antibodies are the correlate of protection in vaccinated individuals enrolled in the Moderna COVE phase 3 clinical trial (see the Perspective by Openshaw). By measuring binding and neutralizing antibodies against the viral spike protein, the authors found that the levels of both antibodies correlated with the degree of vaccine efficacy. The higher the antibody level, the greater the protection afforded by the messenger RNA (mRNA) vaccine. Antibody levels that predict mRNA vaccine efficacy can therefore be used to guide vaccine regimen modifications and support regulatory approvals for a broader spectrum of the population. —PNK
Using correlates to accelerate vaccinology
Authors: Openshaw Peter J. M.
Published: January 2022

Correlates and surrogates of desired outcomes are valuable but have limitations
Richard Lerner (1938–2021)
Authors: Schultz Peter
Published: January 2022

Fearless scientist and leader of Scripps Research
Satellites document rapid expansion of cropland
Authors: Popkin Gabriel
Published: January 2022

Farms added 100 million hectares globally over 2 decades, threatening biodiversity and accelerating climate change
Complete Genome Sequences of Four Putatively Antibiotic-Producing Bacteria Isolated from Soil in Arkansas, USA
Authors: Plymale Ruth , Hopkins Griffin , Johnson Taylor , Savage Taylor , Schaal Danielle
Published: January 2022

Soil bacteria can be a valuable source of antimicrobial compounds. Here, we report the complete genomes of four soil bacteria that were isolated by undergraduate microbiology students as part of a course-based research experience. These genomes were assembled using a hybrid approach combining paired-end Illumina reads with Oxford Nanopore Technologies MinION reads.
Draft Genome Sequence of Streptomyces albidoflavus 09MW18-IS, Cultivated from the Atlantic Ocean off the Coast of Virginia
Authors: Sharma Indu , Washington Masuud , Chen See Jeremy , Suleiman Rola , Lamendella Regina
Published: January 2022

We report a draft genome sequence for
Streptomyces albidoflavus
strain 09MW18-IS, isolated from the Atlantic slope off the coast of Virginia. The whole-genome sequence will provide novel insights into biosynthetic gene clusters and ecological adaptation in an oligotrophic environment.
Draft Genome Sequence of Leifsonia poae Strain BS71, Isolated from a Drought Microcosm
Authors: Ahmed Hanaa , DeAngelis Kristen M. , Morrow Maureen A.
Published: January 2022

We report the draft genome sequence of
Leifsonia poae
strain BS71. This bacterium was isolated from a low soil moisture content model soil microcosm inoculated with forest soil that had been subject to chronic warming.
Draft Genome Sequence of Clostridium bowmanii DSM 14206
T
, Isolated from an Antarctic Microbial Mat
Authors: Palevich Faith P. , Palevich Nikola , Maclean Paul H. , Altermann Eric , Mills John , Brightwell Gale
Published: January 2022

Clostridium bowmanii
type strain DSM 14206 (ATCC BAA-581) was isolated from a microbial mat sample retrieved from Lake Fryxell, Antarctica. This report describes the generation and annotation of the 4.9-Mb draft genome sequence of
C. bowmanii
DSM 14206
T
.
Whole-Genome Sequencing of Streptomycin-Resistant Mycobacterium tuberculosis Strain SBH145 from Sabah, Malaysia
Authors: Mustapha Zainal Arifin , Jani Jaeyres , Stanis Cheronie Shely , Abdull Majid Dg Syahidah Nadiah , Ling Chin Kai , Teo Roddy , Ahmed Kamruddin
Published: January 2022

This paper reports on the whole-genome sequencing of a streptomycin-resistant
Mycobacterium tuberculosis
strain that was isolated from a patient with pulmonary tuberculosis in Sabah state of Malaysian Borneo. The strain belongs to the EAI2-Manila family of lineage 1 and is clustered with
M. tuberculosis
strains from the Philippines, India, and Taiwan.
Complete Genome Sequence of Bacteriophage Fizzles, Isolated from Microbacterium foliorum
Authors: Adams Skyler , Spotz Gabrielle , Babcock Riley , Butler Chloe , Conger Samantha , Crew Madison , Garcia Stephanie , Gonzalez Joanna , Hodges Jocelyn , Martinez Alondra , Munoz Samuel , O’Grady Chloe , Quirl Abigail , Sefcik Kristin , Taylor Tanner , Vazquez Gustavo , Cox Faith , Edwards Dustin
Published: January 2022

Microbacteriophage Fizzles has a 62,078-bp linear double-stranded DNA genome sequence, predicted to contain 104 protein-coding genes. Fizzles is a
Siphoviridae
actinobacteriophage isolated from an ant hill soil sample collected in Stephenville, TX. Microbacteriophage Fizzles has >83.6% nucleotide identity with microbacteriophages Squash and Nike.
Extragenital lichen sclerosus arising in tattooed skin
Authors: Uthayakumar Aarthy Kanmany , Kravvas Georgios , Bunker Christopher Barry
Published: January 2022

Lichen sclerosus (LSc) is a chronic inflammatory condition commonly affecting the anogenital area, with extragenital involvement seen in less than 1%–20% of cases. Concomitant extragenital and genital LSc is extremely rare in male patients. The Koebner phenomenon is a recognised feature of LSc; here we present a rare case of extragenital LSc occurring in tattooed skin.
SARS-CoV-2 antibody prevalence and correlates of six ethnic groups living in Amsterdam, the Netherlands: a population-based cross-sectional study, June–October 2020
Authors: Coyer Liza , Boyd Anders , Schinkel Janke , Agyemang Charles , Galenkamp Henrike , Koopman Anitra D M , Leenstra Tjalling , Moll van Charante Eric P , van den Born Bert-Jan H , Lok Anja , Verhoeff Arnoud , Zwinderman Aeilko H , Jurriaans Suzanne , van Vught Lonneke A , Stronks Karien , Prins Maria
Published: January 2022

Objectives

It has been suggested that ethnic minorities have been disproportionally affected by the COVID-19. We aimed to determine whether prevalence and correlates of past SARS-CoV-2 exposure varied between six ethnic groups in Amsterdam, the Netherlands.

Design, setting, participants

Participants aged 25–79 years enrolled in the Healthy Life in an Urban Setting population-based prospective cohort (n=16 889) were randomly selected within ethnic groups and invited to participate in a cross-sectional COVID-19 seroprevalence substudy.

Outcome measures

We tested participants for SARS-CoV-2-specific antibodies and collected information on SARS-CoV-2 exposures. We estimated prevalence and correlates of SARS-CoV-2 exposure within ethnic groups using survey-weighted logistic regression adjusting for age, sex and calendar time.

Results

Between 24 June and 9 October 2020, we included 2497 participants. Adjusted SARS-CoV-2 seroprevalence was comparable between ethnic Dutch (24/498; 5.1%, 95% CI 2.8% to 7.4%), South-Asian Surinamese (22/451; 4.9%, 95% CI 2.2% to 7.7%), African Surinamese (22/400; 8.3%, 95% CI 3.1% to 13.6%), Turkish (30/408; 7.9%, 95% CI 4.4% to 11.4%) and Moroccan (32/391; 7.2%, 95% CI 4.2% to 10.1%) participants, but higher among Ghanaians (95/327; 26.3%, 95% CI 18.5% to 34.0%). 57.1% of SARS-CoV-2-positive participants did not suspect or were unsure of being infected, which was lowest in African Surinamese (18.2%) and highest in Ghanaians (90.5%). Correlates of SARS-CoV-2 exposure varied across ethnic groups, while the most common correlate was having a household member suspected of infection. In Ghanaians, seropositivity was associated with older age, larger household sizes, living with small children, leaving home to work and attending religious services.

Conclusions

No remarkable differences in SARS-CoV-2 seroprevalence were observed between the largest ethnic groups in Amsterdam after the first wave of infections. The higher infection seroprevalence observed among Ghanaians, which passed mostly unnoticed, warrants wider prevention efforts and opportunities for non-symptom-based testing.
Identification of acute respiratory distress syndrome subphenotypes de novo using routine clinical data: a retrospective analysis of ARDS clinical trials
Authors: Duggal Abhijit , Kast Rachel , Van Ark Emily , Bulgarelli Lucas , Siuba Matthew T , Osborn Jeff , Rey Diego Ariel , Zampieri Fernando G , Cavalcanti Alexandre Biasi , Maia Israel , Paisani Denise M , Laranjeira Ligia N , Serpa Neto Ary , Deliberato Rodrigo Octávio
Published: January 2022

Objectives

The acute respiratory distress syndrome (ARDS) is a heterogeneous condition, and identification of subphenotypes may help in better risk stratification. Our study objective is to identify ARDS subphenotypes using new simpler methodology and readily available clinical variables.

Setting

This is a retrospective Cohort Study of ARDS trials. Data from the US ARDSNet trials and from the international ART trial.

Participants

3763 patients from ARDSNet data sets and 1010 patients from the ART data set.

Primary and secondary outcome measures

The primary outcome was 60-day or 28-day mortality, depending on what was reported in the original trial. K-means cluster analysis was performed to identify subgroups. Sets of candidate variables were tested to assess their ability to produce different probabilities for mortality in each cluster. Clusters were compared with biomarker data, allowing identification of subphenotypes.

Results

Data from 4773 patients were analysed. Two subphenotypes (A and B) resulted in optimal separation in the final model, which included nine routinely collected clinical variables, namely heart rate, mean arterial pressure, respiratory rate, bilirubin, bicarbonate, creatinine, PaO2, arterial pH and FiO2. Participants in subphenotype B showed increased levels of proinflammatory markers, had consistently higher mortality, lower number of ventilator-free days at day 28 and longer duration of ventilation compared with patients in the subphenotype A.

Conclusions

Routinely available clinical data can successfully identify two distinct subphenotypes in adult ARDS patients. This work may facilitate implementation of precision therapy in ARDS clinical trials.
Effectiveness and feasibility of telerehabilitation in patients with COVID-19: a protocol for a systematic review and meta-analysis
Authors: Seid Abubeker Alebachew , Aychiluhm Setognal Birara , Mohammed Ahmed Adem
Published: January 2022

Introduction

Respiratory rehabilitation is the use of exercise, education, and behavioural interventions to alleviate symptoms and improve quality of life. Recent studies highlight that respiratory rehabilitation is effective and safe for patients with COVID-19. We aim to evaluate the effectiveness and feasibility of respiratory telerehabilitation on patients infected with COVID-19 by conducting a systematic review and meta-analysis.

Methods and analysis

PubMed, Web of Science, Science Direct, Physiotherapy Evidence Database, Google Scholar and Cochrane Library databases will be searched from inception to the end of November 2021. Randomised controlled trials investigating the effectiveness of telerehabilitation in the management of COVID-19 will be included. The primary outcomes will be functional capacity, cardiopulmonary exercise tests and quality of life. Secondary outcomes will include anxiety/depression level, sleep quality, mortality rate, completion rate, reason for withdrawal, adverse events, service satisfaction, cost-effectiveness and other potential factors. Two reviewers will independently screen and extract data and perform quality assessment of included studies. The Cochrane risk of bias tool will be used to assess risk of bias. Review Manager V.5.4 (Cochrane Collaboration) software will be used for statistical analysis. Heterogeneity will be analysed using I² statistics. Mean difference or standardised mean difference with 95% CI and p value will be used to calculate treatment effect for outcome variables.

Ethics and dissemination

Ethical approval is not required because this systematic review and meta-analysis is based on previously published data. Final result will be published in peer-reviewed journal and presented at relevant conferences and events.

PROSPERO registration number

CRD42021287975.
Establishing an alternative accommodation for stable hospitalised antepartum patients: barriers and challenges
Authors: Sullivan M Brad , Rentz Abby , Mathura Pamela , Gleddie Megan , Luthra Tania , Thiele Allison T , Kovacs Burns Katharina , Rich Rebecca , Sia Winnie W
Published: January 2022

Background

Patients in remote communities who risk premature delivery require transfer to a tertiary care centre for obstetric and neonatal care. Following stabilisation, many patients are candidates for outpatient management but cannot be discharged to their home communities due to lack of neonatal intensive care unit (ICU) support.

Problem

Without outpatient accommodation proximal to neonatal ICU, these patients face prolonged hospitalisation—an expensive option with medical, social and psychological consequences. Therefore, we sought to establish an alternative accommodation for out-of-town stable antepartum patients.

Methods

Quality Improvement approaches were used to identify process strengths and opportunities for improvement on the antepartum ward in a tertiary care centre. Physician and patient surveys informed outpatient accommodation programme development by a multidisciplinary team. The intervention was implemented using a plan–do–study–act cycle. Barriers to patient discharge and enrolment in the programme were analysed by completing thematic and strengths–weaknesses–opportunities–threats (SWOT) analysis.

Results

Physicians broadly supported safe outpatient management, whereas patients were hesitant to leave the hospital even when physicians assured safety. Our alternative accommodation was pre-existing and cost-effective, however, we encountered significant barriers. The physical space limited family visits and social interaction, lacked desired amenities,and the programme proved inconvenient to patients. The thematic and SWOT analysis identified aspects of the intervention which can be optimised to develop future actionable strategies.

Conclusion

The utilisation of acute care beds is costly for the healthcare system and must be allocated judiciously. Patient needs, experience and health system barriers need to be considered when establishing alternative outpatient accommodations and strategies for stable antepartum patients.
Safety and tolerability of andecaliximab as monotherapy and in combination with an anti-PD-1 antibody in Japanese patients with gastric or gastroesophageal junction adenocarcinoma: a phase 1b study
Authors: Yoshikawa Akie Kimura , Yamaguchi Kensei , Muro Kei , Takashima Atsuo , Ichimura Takashi , Sakai Daisuke , Kadowaki Shigenori , Chin Keisho , Kudo Toshihiro , Mitani Seiichiro , Kitano Shigehisa , Thai Dung , Zavodovskaya Marianna , Liu JieJane , Boku Narikazu , Satoh Taroh
Published: January 2022

Background

Matrix metalloproteinase 9 (MMP9) is implicated in protumorigenic processes. Targeting either stromal or epithelial MMP9 reduces the incidence of metastasis. Andecaliximab is a monoclonal antibody that targets MMP9 with high affinity and selectivity. However, no study has examined whether the inhibition of T-cell programmed death 1 (PD-1) in the presence of andecaliximab increases activated lymphocyte infiltration into the tumor, thereby increasing antitumor activity more than that in anti-PD-1 monotherapy. In this study, we assessed the safety, pharmacokinetics (PK), exploratory biomarkers, and preliminary efficacy of andecaliximab as monotherapy and in combination with nivolumab in Japanese patients with advanced or recurrent gastric or gastroesophageal junction (GEJ) adenocarcinoma.

Methods

This phase 1b study comprised four cohorts enrolling Japanese patients with gastric or GEJ adenocarcinoma. This paper concerns cohorts 1 and 4; cohorts 2 and 3 will be reported subsequently. Cohort 1 enrolled patients with human epidermal growth factor receptor 2 (HER2)-negative tumors (n=8) who received andecaliximab monotherapy (800 mg by intravenous infusion every 2 weeks (Q2W)), and cohort 4 enrolled patients irrespective of their HER2 status (n=10) who received 800 mg of andecaliximab in combination with nivolumab Q2W. Safety, dose-limiting toxicities (DLTs), PK, pharmacodynamics, and biomarkers were assessed in both cohorts.

Results

PK of andecaliximab in Japanese patients with gastric or GEJ adenocarcinoma was similar to that reported in non-Japanese patients with advanced solid tumors. Andecaliximab monotherapy and in combination with nivolumab demonstrated no DLTs in cohort 1 and 4, respectively. Toxicities were manageable and well tolerated in both cohorts. The median progression-free survival was 1.4 months (90% CI, 0.5 to 5.4) and 4.6 months (90% CI, 0.9 to not reached) in cohorts 1 and 4, respectively. The objective response rate was 50% (90% CI, 22% to 78%) in cohort 4, and in some patients, the combination therapy was effective regardless of the biomarker status.

Conclusions

The andecaliximab–nivolumab combination demonstrated a manageable safety profile and promising clinical activity in patients with advanced gastric adenocarcinoma.

NCT02862535.
COVID-19 vaccination status should not be used in triage tie-breaking
Authors: Schuman Olivia , Robertson-Preidler Joelle , Bibler Trevor M
Published: January 2022

This article discusses the triage response to the COVID-19 delta variant surge of 2021. One issue that distinguishes the delta wave from earlier surges is that by the time it became the predominant strain in the USA in July 2021, safe and effective vaccines against COVID-19 had been available for all US adults for several months. We consider whether healthcare professionals and triage committees would have been justified in prioritising patients with COVID-19 who are vaccinated above those who are unvaccinated in first-order or second-order triage. Given that lack of evidence for a correlation between short-term survival and vaccination, we argue that using vaccination status during first-order triage would be inconsistent with accepted triage standards. We then turn to notions of procedural fairness, equity and desert to argue that that there is also a lack of justification for using vaccination status in second-order triage. In planning for future surges, we recommend that medical institutions base their triage decisions on principles meant to save the most lives, minimise inequity and protect the public’s trust, which for the time being would not be served by the inclusion of vaccination status.
Differences between sperm sharing and egg sharing are morally relevant
Authors: Hodson Nathan
Published: January 2022

Sperm sharing arrangements involve a man (‘the sharer’) allowing his sperm to be used by people seeking donor sperm (‘the recipients’) in exchange for reduced price in vitro fertilisation. Clinics in the UK have offered egg sharing since the 1990s and the arrangement has been subjected to regulatory oversight and significant ethical analysis. By contrast, until now no published ethical or empirical research has analysed sperm sharing. Moreover the Human Fertilisation and Embryology Authority (HFEA) does not record the number of sperm sharing arrangements taking place.

This paper describes the sperm sharing process providing an analysis of all the UK clinics advertising sperm sharing services. The ethical rationale for egg sharing is described: reducing the number of women exposed to the risks of stimulation and retrieval. This advantage is absent in sperm sharing where donation has no physical drawbacks. The key adverse social and emotional outcome of gamete sharing arises when the sharer’s own treatment is unsuccessful and the recipient’s is successful. This outcome is more likely in sperm sharing than in egg sharing given sperm from sharers can be used by up to 10 families whereas shared eggs only go to one other family.

Given its morally relevant differences from egg sharing, sperm sharing requires its own ethical analysis. The HFEA should begin recording sperm sharing arrangements in order to enable meaningful ethical and policy scrutiny.
Privacy, autonomy and direct-to-consumer genetic testing: a response to Vayena
Authors: van Oosterum Kyle
Published: January 2022

In Vayena’s article, ‘direct-to-consumer (DTC) genomics on the scales of autonomy’, she claims that there may be a strong autonomy-based argument for permitting DTC genomic services. In this response, I point out how the diminishment of one’s genetic privacy can cause a relevant autonomy-related harm which must be balanced against the autonomy-related gains DTC services provide. By drawing on conceptual connections between privacy and the Razian conception of autonomy, I show that DTC genetic testing may decrease the range of valuable options individuals possess, which impacts the extent to which would-be consumers can exercise their autonomy.
Hypospadias in toddlers: a multivariable study of prognostic factors in distal to mid-shaft hypospadias and review of literature
Authors: Roshandel M Reza , Aghaei Badr Tannaz , Kazemi Rashed Fahimeh , Salomon Samantha , Ghahestani Seyyed Mohammad , Ferrer Fernando A
Published: January 2022

Background

Tubularized incised plate urethroplasty is the most common hypospadias repair technique. However, there are unanswered questions and debates about the anatomical prognostic factors affecting the repair outcomes. This study tried to address some of the problems in the studies compromising the results of the current body of literature.

Methods

A prospective cohort of 101 males aged 1–3 years undergoing primary distal to mid-shaft hypospadias repair were enrolled in the study. Complications including edema, erection, inadvertent removal of the urethral stent, surgical wound infection, bladder spasm, hematoma, and hemorrhage were evaluated. Studies in the current literature were reviewed to achieve a better perspective for future investigations.

Results

Persistent complications were found in 16 cases (15.8%) including fistula formation, the persistence of chordee, meatal stenosis, glans, and urethral dehiscence. The mean follow-up time was 6.6±3.4 months. In the single-variable analysis, the meatal location, the length and width of the urethral plate, and the reversible acute postoperative events were significantly associated with the complications. Furthermore, fistula formation was associated with acute surgical site infection (p<0.001). However, the multivariable regression study revealed the presurgical meatal location to be the only statistically significant factor (p=0.03). Notably, the glans diameter or glanular groove shape, urethral plate dimensions, or presence of mild chordee were not independently associated with the outcomes (p>0.05).

Conclusions

Our study on the toddlers with hypospadias surgery revealed that the location of urethral meatal was the main predicting factor in the development of major complications. Furthermore, the fistula formation at the infected surgical site emphasizes the importance of postsurgical care.
Prenatal administration of heparin-binding epidermal growth factor-like growth factor in an experimental model of necrotizing enterocolitis decreased both incidence and severity of the disease
Authors: Sacks Marla Ashley , Mendez Yomara Stephanie , Khan Faraz A , Propst Robert , Zuppan Craig W , Wilson Christopher G , Radulescu Andrei
Published: January 2022

Background

Necrotizing enterocolitis (NEC) is the leading gastrointestinal cause of death in premature infants and causes long-term disabilities. Previously, enteral heparin-binding epidermal growth factor-like growth factor (HB-EGF) administered after birth demonstrated decreased incidence and severity of NEC in a neonatal animal model of NEC. We investigated the potential prophylactic strategy of preventing NEC using prenatally administered HB-EGF.

Methods

An HB-EGF (800 µg/kg/dose) dose was injected into pregnant rats via tail vein or intraperitoneal route 2 hours prior to delivery. After cesarean section (C-section) at 21 days’ gestation, the rat pups were subjected to the NEC protocol by inducing stressors: hypoxia, hypothermia, hypertonic feeds, and orogastric gavage of lipopolysaccharide (2 mg/kg). Postnatally, pups were monitored for 96 hours and assessed for the development of clinical and postmortem histological NEC.

Results

The experimental NEC incidence in untreated, stressed rat pups was 66%. Compared with untreated pups, the maternal administration of HB-EGF correlated with a significant NEC incidence and severity decrease in rat pups. The strongest decrease was seen when HB-EGF was administered via the intraperitoneal route 2 hours prior to C-section (66% vs 31%, *p<0.05). Prenatal HB-EGF administration significantly increased pups’ survival after NEC protocol exposure, with the greatest benefit observed in the group that received HB-EGF intraperitoneally 2 hours before delivery.

Conclusions

Prenatal administration of HB-EGF decreases the incidence and severity of NEC, preserves gut barrier function and increases survival. This may represent a novel prophylactic clinical strategy for NEC offered to mothers at risk of delivering a premature infant.
Effect of soya phosphatidylcholine and possible underlying mechanism on ischemia/reperfusion injury in isolated perfused rat heart: an experimental and computational study
Authors: Mehta Anita A. , Patel Purav , Thakur Vandana R. , Beladiya Jayesh V.
Published: January 2022

This study was designed to assess the effect of soya phosphatidylcholine (SPC) against ischemia/reperfusion (I/R) injury and the possible underlying mechanism using experimental and computational studies. I/R injury was induced by global ischemia for 30 min followed by reperfusion for 120 min. The perfusion of the SPC was performed for 10 min before inducing global ischemia. In the mechanistic study, the involvement of specific cellular pathways was identified using various inhibitors such as ATP-dependent potassium channel (KATP) inhibitor (glibenclamide), protein kinase C (PKC) inhibitor (chelerythrine), non-selective nitric oxide synthase inhibitor (L-NAME), and endothelium remover (Triton X-100). The computational study of various ligands was performed on toll-like receptor 4 (TLR4) protein using AutoDock version 4.0. SPC (100 μM) significantly decreased the levels of cardiac damage markers and %infarction compared with the vehicle control (VC). Furthermore, cardiodynamics (indices of left ventricular contraction (dp/dtmax), indices of left ventricular relaxation (dp/dtmin), coronary flow, and antioxidant enzyme levels were significantly improved as compared with VC. This protective effect was attenuated by glibenclamide, chelerythrine, and Triton X-100, but it was not attenuated by L-NAME. The computational study showed a significant bonding affinity of SPC to the TLR4-MD2 complex. Thus, SPC reduced myocardial I/R injury in isolated perfused rat hearts, which might be governed by the KATP channel, PKC, endothelium response, and TLR4-MyD88 signaling pathway.
A Virtual Reality Application of the Rubber Hand Illusion Induced by Ultrasonic Mid-air Haptic Stimulation
Authors: Salagean Anca , Hadnett-Hunter Jacob , Finnegan Daniel J. , De Sousa Alexandra A. , Proulx Michael J.
Published: January 2022

Ultrasonic mid-air haptic technologies, which provide haptic feedback through airwaves produced using ultrasound, could be employed to investigate the sense of body ownership and immersion in virtual reality (VR) by inducing the virtual hand illusion (VHI). Ultrasonic mid-air haptic perception has solely been investigated for glabrous (hairless) skin, which has higher tactile sensitivity than hairy skin. In contrast, the VHI paradigm typically targets hairy skin without comparisons to glabrous skin. The aim of this article was to investigate illusory body ownership, the applicability of ultrasonic mid-air haptics, and perceived immersion in VR using the VHI. Fifty participants viewed a virtual hand being stroked by a feather synchronously and asynchronously with the ultrasonic stimulation applied to the glabrous skin on the palmar surface and the hairy skin on the dorsal surface of their hands. Questionnaire responses revealed that synchronous stimulation induced a stronger VHI than asynchronous stimulation. In synchronous conditions, the VHI was stronger for palmar stimulation than dorsal stimulation. The ultrasonic stimulation was also perceived as more intense on the palmar surface compared to the dorsal surface. Perceived immersion was not related to illusory body ownership per se but was enhanced by the provision of synchronous stimulation.
Real-Time Cooling Power Attribution for Co-Located Data Center Rooms with Distinct Temperatures and Humidities
Authors: Wang Rongrong , Van Le Duc , Tan Rui , Wong Yew-Wah
Published: January 2022

At present, a co-location data center often applies an identical and low temperature setpoint for its all server rooms. Although increasing the temperature setpoint is a rule-of-thumb approach to reducing the cooling energy usage, the tenants may have different mentalities and technical constraints in accepting higher temperature setpoints. Thus, supporting distinct temperature setpoints is desirable for a co-location data center in pursuing higher energy efficiency. This calls for a new cooling power attribution scheme to address the inter-room heat transfers that can be up to 9% of server load as shown in our real experiments. This article describes our approaches to estimating the inter-room heat transfers, using the estimates to rectify the metered power usages of the rooms’ air handling units, and fairly attributing the power usage of the shared cooling infrastructure (i.e., chiller and cooling tower) to server rooms by following the Shapley value principle. Extensive numeric experiments based on a widely accepted cooling system model are conducted to evaluate the effectiveness of the proposed cooling power attribution scheme. A case study suggests that the proposed scheme incentivizes rational tenants to adopt their highest acceptable temperature setpoints under a non-cooperative game setting. Further analysis considering distinct relative humidity setpoints shows that our proposed scheme also properly and inherently addresses the attribution of humidity control power.
Detection and Mitigation of Sensor and CAN Bus Attacks in Vehicle Anti-Lock Braking Systems
Authors: Kang Liuwang , Shen Haiying
Published: January 2022

For a modern vehicle, if the sensor in a vehicle anti-lock braking system (ABS) or controller area network (CAN) bus is attacked during a brake process, the vehicle will lose driving direction control and the driver’s life will be highly threatened. However, current methods for detecting attacks are not sufficiently accurate, and no method can provide attack mitigation. To ensure vehicle ABS security, we propose an attack detection method to accurately detect both sensor attack (SA) and CAN bus attack in a vehicle ABS, and an attack mitigation strategy to mitigate their negative effects on the vehicle ABS. In our attack detection method, we build a vehicle state space equation that considers the real-time road friction coefficient to predict vehicle states (i.e., wheel speed and longitudinal brake force) with their previous values. Based on sets of historical measured vehicle states, we develop a search algorithm to find out attack changes (vehicle state changes because of attack) by minimizing errors between the predicted vehicle states and the measured vehicle states. In our attack mitigation strategy, attack changes are subtracted from the measured vehicle states to generate correct vehicle states for a vehicle ABS. We conducted the first real SA experiments to show how a magnet affects sensor readings. Our simulation results demonstrate that our attack detection method can detect SA and CAN bus attack more accurately compared with existing methods, and also that our attack mitigation strategy almost eliminates the attack’s effects on a vehicle ABS.
A Systematic Review on Data Scarcity Problem in Deep Learning: Solution and Applications
Authors: Bansal Ms. Aayushi , Sharma Dr. Rewa , Kathuria Dr. Mamta
Published: January 2022

Recent advancements in deep learning architecture have increased its utility in real-life applications. Deep learning models require a large amount of data to train the model. In many application domains, there is a limited set of data available for training neural networks as collecting new data is either not feasible or requires more resources such as in marketing, computer vision, and medical science. These models require a large amount of data to avoid the problem of overfitting. One of the data space solutions to the problem of limited data is data augmentation. The purpose of this study focuses on various data augmentation techniques that can be used to further improve the accuracy of a neural network. This saves the cost and time consumption required to collect new data for the training of deep neural networks by augmenting available data. This also regularizes the model and improves its capability of generalization. The need for large datasets in different fields such as computer vision, natural language processing, security, and healthcare is also covered in this survey paper. The goal of this paper is to provide a comprehensive survey of recent advancements in data augmentation techniques and their application in various domains.
Transformers in Vision: A Survey
Authors: Khan Salman , Naseer Muzammal , Hayat Munawar , Zamir Syed Waqas , Khan Fahad Shahbaz , Shah Mubarak
Published: January 2022

Astounding results from Transformer models on natural language tasks have intrigued the vision community to study their application to computer vision problems. Among their salient benefits, Transformers enable modeling long dependencies between input sequence elements and support parallel processing of sequence as compared to recurrent networks, e.g., Long short-term memory. Different from convolutional networks, Transformers require minimal inductive biases for their design and are naturally suited as set-functions. Furthermore, the straightforward design of Transformers allows processing multiple modalities (e.g., images, videos, text, and speech) using similar processing blocks and demonstrates excellent scalability to very large capacity networks and huge datasets. These strengths have led to exciting progress on a number of vision tasks using Transformer networks. This survey aims to provide a comprehensive overview of the Transformer models in the computer vision discipline. We start with an introduction to fundamental concepts behind the success of Transformers, i.e., self-attention, large-scale pre-training, and bidirectional feature encoding. We then cover extensive applications of transformers in vision including popular recognition tasks (e.g., image classification, object detection, action recognition, and segmentation), generative modeling, multi-modal tasks (e.g., visual-question answering, visual reasoning, and visual grounding), video processing (e.g., activity recognition, video forecasting), low-level vision (e.g., image super-resolution, image enhancement, and colorization), and three-dimensional analysis (e.g., point cloud classification and segmentation). We compare the respective advantages and limitations of popular techniques both in terms of architectural design and their experimental value. Finally, we provide an analysis on open research directions and possible future works. We hope this effort will ignite further interest in the community to solve current challenges toward the application of transformer models in computer vision.
Seismic Advances in Process Geomorphology
Authors: Cook Kristen L. , Dietze Michael
Published: January 2022

One of the pillars of geomorphology is the study of geomorphic processes and their drivers, dynamics, and impacts. Like all activity that transfers energy to Earth's surface, a wide range of geomorphic process types create seismic waves that can be measured with standard seismic instruments. Seismic signals provide continuous high-resolution coverage with a spatial footprint that can vary from local to global, and in recent years, efforts to exploit these signals for information about surface processes have increased dramatically, coalescing into the emerging field of environmental seismology. The application of seismic methods has the potential to drive advances in our understanding of the occurrence, timing, and triggering of geomorphic events, the dynamics of geomorphic processes, fluvial bedload transport, and integrative geomorphic system monitoring. As new seismic applications move from development to proof of concept to routine application, integration between geomorphologists and seismologists is key for continued progress. ▪ Geomorphic activity on Earth's surface produces seismic signals that can be measured with standard seismic instruments. ▪ Seismic methods are driving advances in our understanding of the occurrence, triggering, and internal dynamics of a range of geomorphic processes. ▪ Dedicated seismic-based observatories offer the potential to comprehensively characterize geomorphic activity and its impacts across a landscape. ▪ Collaboration between seismologists and geomorphologists is fostering the development of new applications, models, and analysis techniques for geomorphic seismology.
The Gut Microbiome as a Regulator of the Neuroimmune Landscape
Authors: Yu Lewis W. , Agirman Gulistan , Hsiao Elaine Y.
Published: January 2022

The gut microbiome influences many host physiologies, spanning gastrointestinal function, metabolism, immune homeostasis, neuroactivity, and behavior. Many microbial effects on the host are orchestrated by bidirectional interactions between the microbiome and immune system. Imbalances in this dialogue can lead to immune dysfunction and immune-mediated conditions in distal organs including the brain. Dysbiosis of the gut microbiome and dysregulated neuroimmune responses are common comorbidities of neurodevelopmental, neuropsychiatric, and neurological disorders, highlighting the importance of the gut microbiome–neuroimmune axis as a regulator of central nervous system homeostasis. In this review, we discuss recent evidence supporting a role for the gut microbiome in regulating the neuroimmune landscape in health and disease.
Patient Centricity Driving Formulation Innovation: Improvements in Patient Care Facilitated by Novel Therapeutics and Drug Delivery Technologies
Authors: Page Susanne , Khan Tarik , Kühl Peter , Schwach Gregoire , Storch Kirsten , Chokshi Hitesh
Published: January 2022

Innovative formulation technologies can play a crucial role in transforming a novel molecule to a medicine that significantly enhances patients’ lives. Improved mechanistic understanding of diseases has inspired researchers to expand the druggable space using new therapeutic modalities such as interfering RNA, protein degraders, and novel formats of monoclonal antibodies. Sophisticated formulation strategies are needed to deliver the drugs to their sites of action and to achieve patient centricity, exemplified by messenger RNA vaccines and oral peptides. Moreover, access to medical information via digital platforms has resulted in better-informed patient groups that are requesting consideration of their needs during drug development. This request is consistent with health authority efforts to upgrade their regulations to advance age-appropriate product development for patients. This review describes formulation innovations contributingto improvements in patient care: convenience of administration, preferred route of administration, reducing dosing burden, and achieving targeted delivery of new modalities.
Central Nervous System Control of Glucose Homeostasis: A Therapeutic Target for Type 2 Diabetes?
Authors: Mirzadeh Zaman , Faber Chelsea L. , Schwartz Michael W.
Published: January 2022

Historically, pancreatic islet beta cells have been viewed as principal regulators of glycemia, with type 2 diabetes (T2D) resulting when insulin secretion fails to compensate for peripheral tissue insulin resistance. However, glycemia is also regulated by insulin-independent mechanisms that are dysregulated in T2D. Based on evidence supporting its role both in adaptive coupling of insulin secretion to changes in insulin sensitivity and in the regulation of insulin-independent glucose disposal, the central nervous system (CNS) has emerged as a fundamental player in glucose homeostasis. Here, we review and expand upon an integrative model wherein the CNS, together with the islet, establishes and maintains the defended level of glycemia. We discuss the implications of this model for understanding both normal glucose homeostasis and T2D pathogenesis and highlight centrally targeted therapeutic approaches with the potential to restore normoglycemia to patients with T2D.
Li-Ion Cell Safety Monitoring Using Mechanical Parameters: Part I. Normal Battery Operation
Authors: Kirchev A. , Guillet N. , Brun-Buission D. , Gau V.
Published: January 2022

The normal operation of a 18650 lithium-ion cells has been monitored using rectangular rosette strain gauge and a pair of piezoelectric transducers. The sensors for mechanical measurements provide information about the cell deformation mechanism and electrodes structure during the cycling. The strain gauge signal revealed three type of mechanical processes. The predominant deformation pattern during galvanostatic discharge process is an isotropic cylindrical shrinkage relevant to the extraction of lithium ions from the graphite negative electrode. In the case of low-rate discharge in cyclic voltammetry mode, the deformation pattern changes to spherical growth when the state of charge falls below 40. In contrast, the thermal shrinkage and growth of the cell corresponds to simple decrease of the cell diameter with much smaller hysteresis effect. The ultrasound interrogation is able to detect repeatable progressive change of the acoustic waveform transferred across the cell in direction of the jellyroll diameter, which depends on the state of charge and does not undergo any significant changes at different cycling rates. The impact of the state of health under 2 h—rated charge/discharge cycling at 25 °C reveals slow progressive drift of the strain and acoustic signals corresponding to the growth of the cell size.
From Bunsen to VLSI
Authors: Allendorf Mark
Published: January 2022

With these dramatic words, the German chemist Bunsen began an account in 1852 in which he described his observation that iron oxide condenses as crystals from hot volcanic gases containing hydrogen chloride (HCl).