bluuebunny/crossref_metadata_2025 huggingface dataset:
Relative frequency of drug-induced sleep disorders for 32 antidepressants in a large set of Internet user reviews
Authors: Natter Johan , Yokoyama Taïoh , Michel Bruno
Published: July 2021

Study Objectives

It is known that antidepressant drugs can induce sleep disorders in patients, but little data exist about high or low-risk molecules. The aim was to study the frequency of antidepressant drug-induced sleep disorders (DISD) by molecule.

Methods

77,391 patient comments for 32 antidepressant drugs were collected from drug review websites and screened for DISD. Association between drugs and nightmare disorder, restless legs syndrome, sleep paralysis, sleep terrors, sleep-related hallucinations, or sleep walking was expressed as relative proportion [proportional reporting ratio (PRR)]. A detailed analysis of the content of the dreams was also carried out.

Results

Amitriptyline, doxepin, fluvoxamine, mirtazapine, nortriptyline, trazodone, venlafaxine, and vilazodone were associated with a greater frequency of DISD compared to other antidepressants. Vilazodone heavily increased the probability of developing 5 of the 6 studied DISD (PRR 3.3 to 19.3) and mirtazapine increased the probability of developing 4 DISD (PRR 2.4 to 6.4). Bupropion and citalopram were associated with lower probabilities for 5 DISD (PRR 0.2 to 0.7). Sentiment analysis showed that patients described disturbing dreams for vilazodone or mirtazapine and strange but less negative dreams for bupropion, citalopram, or duloxetine.

Conclusions

Relative frequencies of sleep disorders were obtained for a vast panel of antidepressant drugs through an original analysis of user’s drug reviews on drug rating websites. Our results could guide clinicians in the appropriate choice of antidepressant drugs for high DISD-risk patients in need of such treatment. These results may however be cautiously taken, considering the uncertain reliability and generalizability of web-based data.
Cdc25B is transcriptionally inhibited by IER5 through the NF-YB transcription factor in irradiation-treated HeLa cells
Authors: Ding Lixin , Zhao Xianzhe , Xiong Qiang , Jiang Xiaoyan , Liu Xiaodan , Ding Kuke , Zhou Pingkun
Published: July 2021

Cervical cancer (CC) is a type of pelvic malignant tumor that severely threatens women's health. Current evidence suggests that IER5, as a potential radiosensitizer, promotes irradiation-induced apoptosis in CC tissues in patients undergoing chemoradiotherapy. IER5 has been shown to be involved in the G2/M-phase transition. In the present study, we used Cdc25B as the breakthrough point to explore the underlying mechanism of IER5 in the cell cycle regulation of radiation-damaged HeLa cells. IER5 was evidently upregulated after irradiation, but Cdc25B was significantly downregulated. In monoclonal IER5-silenced HeLa cells, irradiation-induced downregulation of Cdc25B was attenuated. The effect of irradiation on Cdc25B promoter activity was determined by dual-luciferase reporter assays. The response elements on the Cdc25B promoter related to irradiation were predicted by JASPAR. These conserved sequences were mutated individually or in combination by splicing-by-overlap extension PCR, and their function was confirmed by dual-luciferase reporter assays. The enrichment efficiency of transcription factors after irradiation was determined by chromatin immunoprecipitation (ChIP) assay. Both Sp1/Sp3 and NF-YB binding sites were involved in irradiation-mediated regulation of Cdc25B. IER5 was involved in irradiation-mediated regulation of Cdc25B through the NF-YB binding site. Furthermore, ChIP assays showed that IER5 bound to the Cdc25B promoter, and the binding of IER5 to the Cdc25B promoter region in irradiation-induced HeLa cells induced the release of the coactivator p300 through interaction with NF-YB. Taken together, these findings indicate that IER5 is the transcriptional repressor that accelerates the downregulation of Cdc25B expression after irradiation.
A misinterpreted disjunction: the phylogenetic relationships of the North African land snail Gyrostomella (Gastropoda: Stylommatophora: Helicidae)
Authors: Neiber Marco T , Korábek Ondřej , Glaubrecht Matthias , Hausdorf Bernhard
Published: July 2021

The North African helicid Gyrostomella has been considered closely related to Levantina, suggesting a disjunct distribution with a distribution gap of almost 2000 km in North Africa. We studied this disjunction and the systematics of Helicinae using molecular markers. Our analyses indicate an affiliation of Gyrostomella with the radiation of Helicinae in the Maghreb, especially with Maurohelix. The occurrence of Gyrostomella in Libya does not represent a western outpost of Helicini in North Africa, but an eastern outpost of the Maghreb radiation of Helicinae. The disjunction of Gyrostomella in Libya and Maurohelix in Algeria may be the result of a long-distance dispersal or may represent relicts of a larger range of the lineage in the past as a consequence of aridification processes in North Africa. Taking into account biogeographic patterns, we suggest a subdivision of Helicinae into four tribes: Allognathini, Helicini, Maculariini trib. nov. and Thebini. The Eastern Mediterranean Helicini diverged from the Western Mediterranean clade in the Eocene. The Western Mediterranean clade then split into Allognathini in the Iberian Peninsula, Maculariini in the region of the future western Alps and Thebini on terranes probably including the Rif-Betic and Kabylies blocks that now form part of the Maghreb region.
Best Clinical Practices with ATX-101 for Submental Fat Reduction: Patient-related Factors and Physician Considerations
Authors: Teller Craig F. , Chiu Annie , Chesnut Cameron D. , Sherman Deborah , Raul Montes José , Gaspard Sara , Keaney Terrence , Sadick Neil S. , Yoelin Steve , Sangha Sara , Shridharani Sachin M.
Published: July 2021

Background:

Submental fat can be reduced with ATX-101 (deoxycholic acid injection), a customizable and minimally invasive alternative to liposuction. In the years since its approval, the treatment patterns of ATX-101 have evolved.

Methods:

A panel of experienced physicians from the United States gathered to generate best practices for the use of ATX-101 in submental contouring.

Results:

The expert panel provided their insights on appropriate patient selection, managing patient expectations of ATX-101 treatment outcomes, and adverse events, and guidance on ATX-101 administration for optimal outcomes are presented here.

Conclusion:

These best clinical practices on the use of ATX-101 for the reduction of submental fat should enable physicians to enhance the patient treatment experience and outcomes.
How to Get Consistently Good Results in Cleft Lip Repair
Authors: Kamel George N. , Segal Rachel M. , Tsai Catherine , Kordahi Anthony , Gosman Amanda A.
Published: July 2021

This article serves as a practical guide for plastic surgeons focusing on repair of primary cleft lip and nasal deformity. We discuss the key anatomic disruption present in cleft lip and nasal deformity and the goals of primary repair. In addition, our preferred surgical technique for unilateral and bilateral cleft lip and nasal deformity is summarized along with technical pearls and pitfalls.
Combined Sequential Bilateral Hypoglossal-to-facial and Masseter-to-facial Transfers for Bilateral Facial Paralysis
Authors: Morales-Puebla Jose M. , González-Otero Teresa , Moraleda Susana , Santiago Susana , Gavilán Javier , Lassaletta Luis
Published: July 2021

Bilateral facial paralysis is a challenging situation requiring complex management. Surgical treatment can include nerve transfers, mainly masseter-to-facial, or muscle transfers, gracilis free flap, or temporalis transposition. Deciding on the surgical option depends on the duration of the paralysis and the feasibility of facial muscles. We present the case of a 10-year-old child with permanent bilateral facial paralysis after brainstem tumor surgery. The patient was treated with bilateral simultaneous hypoglossal-to-facial transfer followed by bilateral simultaneous masseter-to-facial 12 months later. After 23 months of follow-up and specific physical therapy, she has good and symmetric resting tone, complete eye closure, moderate bilateral smile excursion, mild lip pucker movement, and good oral competence. The combination of these two nerve transfers, when possible, gives the opportunity of restoring movement taking the best of each technique, with acceptable results and no significant clinical deficits in the donor sites.
Performance of RT-PCR on Saliva Specimens Compared With Nasopharyngeal Swabs for the Detection of SARS-CoV-2 in Children
Authors: Fougère Yves , Schwob Jean Marc , Miauton Alix , Hoegger Francesca , Opota Onya , Jaton Katia , Brouillet Rene , Greub Gilbert , Genton Blaise , Gehri Mario , Taddeo Ilaria , D’Acremont Valérie , Asner Sandra A.
Published: July 2021

Background:

Saliva reverse transcriptase-Polymerase chain reaction (RT-PCR) is an attractive alternative for the detection of severe acute respiratory syndrome coronavirus 2 in adults with less known in children.

Methods:

Children with coronavirus disease 2019 symptoms were prospectively enrolled in a 1-month comparative clinical trial of saliva and nasopharyngeal (NP) RT-PCR. Detection rates and sensitivities of saliva and NP RT-PCR were compared as well as discordant NP and saliva RT-PCR findings including viral loads (VLs).

Results:

Of 405 patients enrolled, 397 patients had 2 tests performed. Mean age was 12.7 years (range, 1.2–17.9). Sensitivity of saliva was 85.2% (95% confidence interval: 78.2%–92.1%) when using NP as the standard; sensitivity of NP was 94.5% (89.8%–99.2%) when saliva was considered as the standard. For a NP RT-PCR VL threshold of ≥103 and ≥104 copies/mL, sensitivity of saliva increases to 88.7% and 95.2%, respectively. Sensitivity of saliva and NP swabs was, respectively, 89.5% and 95.3% in patient with symptoms less than 4 days (P = 0.249) and 70.0% and 95.0% in those with symptoms ≥4–7 days (P = 0.096). The 15 patients who had an isolated positive NP RT-PCR were younger (P = 0.034), had lower NP VL (median 5.6 × 103 vs. 3.9 × 107, P < 0.001), and could not drool saliva at the end of the sampling (P = 0.002). VLs were lower with saliva than with NP RT-PCR (median 8.7 cp/mL × 104; interquartile range 1.2 × 104–5.2 × 105; vs. median 4.0 × 107 cp/mL; interquartile range, 8.6 × 105–1 × 108; P < 0.001).

Conclusions:

While RT-PCR testing on saliva performed more poorly in younger children and likely after longer duration of symptoms, saliva remains an attractive alternative to NP swabs in children.
A Bayesian Model to Predict COVID-19 Severity in Children
Authors: Domínguez-Rodríguez Sara , Villaverde Serena , Sanz-Santaeufemia Francisco J. , Grasa Carlos , Soriano-Arandes Antoni , Saavedra-Lozano Jesús , Fumadó Victoria , Epalza Cristina , Serna-Pascual Miquel , Alonso-Cadenas José A. , Rodríguez-Molino Paula , Pujol-Morro Joan , Aguilera-Alonso David , Simó Silvia , Villanueva-Medina Sara , Iglesias-Bouzas M. Isabel , Mellado M. José , Herrero Blanca , Melendo Susana , De la Torre Mercedes , Del Rosal Teresa , Soler-Palacin Pere , Calvo Cristina , Urretavizcaya-Martínez María , Pareja Marta , Ara-Montojo Fátima , Ruiz del Prado Yolanda , Gallego Nerea , Illán Ramos Marta , Cobos Elena , Tagarro Alfredo , Moraleda Cinta ,   on behalf of EPICO-AEP Working Group
Published: July 2021

Background:

We aimed to identify risk factors causing critical disease in hospitalized children with COVID-19 and to build a predictive model to anticipate the probability of need for critical care.

Methods:

We conducted a multicenter, prospective study of children with SARS-CoV-2 infection in 52 Spanish hospitals. The primary outcome was the need for critical care. We used a multivariable Bayesian model to estimate the probability of needing critical care.

Results:

The study enrolled 350 children from March 12, 2020, to July 1, 2020: 292 (83.4%) and 214 (73.7%) were considered to have relevant COVID-19, of whom 24.2% required critical care. Four major clinical syndromes of decreasing severity were identified: multi-inflammatory syndrome (MIS-C) (17.3%), bronchopulmonary (51.4%), gastrointestinal (11.6%), and mild syndrome (19.6%). Main risk factors were high C-reactive protein and creatinine concentration, lymphopenia, low platelets, anemia, tachycardia, age, neutrophilia, leukocytosis, and low oxygen saturation. These risk factors increased the risk of critical disease depending on the syndrome: the more severe the syndrome, the more risk the factors conferred. Based on our findings, we developed an online risk prediction tool (https://rserver.h12o.es/pediatria/EPICOAPP/, username: user, password: 0000).

Conclusions:

Risk factors for severe COVID-19 include inflammation, cytopenia, age, comorbidities, and organ dysfunction. The more severe the syndrome, the more the risk factor increases the risk of critical illness. Risk of severe disease can be predicted with a Bayesian model.
Soft tissue impingement at the femorotibial joint after a posterior cruciate ligament-retaining total knee arthroplasty
Authors: Nakamura Mitsuhiro , Soda Yoshinori , Adachi Nobuo
Published: July 2021

Introduction:

Impingement of soft tissue at the femorotibial (FT) joint after a total knee arthroplasty (TKA) can lead to poor postoperative performance and pain. In this report, we have described a case of FT joint impingement by scar tissue formation extending over the anterior surface of the intercondylar fossa after a posterior cruciate ligament (PCL)-retaining TKA.

Patient concerns:

A 78-year-old woman developed crepitations and discomfort during left knee extension and stair climbing at about 10 months after TKA.

Diagnosis:

Plain radiographs of her knee revealed that the patella baja present from before her TKA had progressed. Impression marks in the distal pole of the patella caused by the impingement of the scar tissue between the femoral component of PCL-retaining TKA and the PCL insertion during knee extension were also observed. The impingement was confirmed by direct arthroscopy.

Interventions:

We treated her by performing a resection of the scar tissue, excision of the distal pole of the patella, and replacement of the patella.

Outcomes:

Recovery period was unremarkable, with no recurrence of symptoms over the subsequent 5-year follow-up period.

Conclusion:

Our case demonstrates that a chronic mechanical irritation can induce proliferation of the residual synovial tissue at the insertion of the PCL. This, in turn, could result in the growth of a scar-like tissue, which could extend over the anterior surface of the intercondylar fossa and grow into the distal pole of the patella, causing an impingement at the FT joint. The presence of a patella baja before TKA could be a risk factor for FT impingement after PCL-retaining TKA, warranting a careful follow-up of these patients.
Targeting zero preventable trauma readmissions
Authors: Neiman Pooja U. , Brown Craig S. , Montgomery John R. , Sangji Naveen F. , Hemmila Mark R. , Scott John W.
Published: July 2021

BACKGROUND

Nearly 1-in-10 trauma patients in the United States are readmitted within 30 days of discharge, with a median hospital cost of more than $8,000 per readmission. There are national efforts to reduce readmissions in trauma care, but we do not yet understand which are potentially preventable. Our study aims to quantify the potentially preventable readmissions (PPRs) in trauma care to serve as the anchor point for ongoing efforts to curb hospital readmissions and ultimately, bring preventable readmissions to zero.

METHODS

We identified inpatient hospitalizations after trauma and readmissions within 90 days in the 2017 National Readmissions Database (NRD). Potentially preventable readmissions were defined as the Agency for Healthcare Research and Quality–defined Ambulatory Care Sensitive Conditions, in addition to superficial surgical site infection, acute kidney injury/acute renal failure, and aspiration pneumonitis. Mean costs for these admissions were calculated using the NRD. A multivariable logistic regression model was used to characterize the relationship between patient characteristics and PPR.

RESULTS

A total of 1,320,083 patients were admitted for trauma care in the 2017 NRD, and 137,854 (10.4%) were readmitted within 90 days of discharge. Of these readmissions, 22.7% were potentially preventable. The mean cost was $10,001/PPR, resulting in $313,802,278 in cost to the US health care system. Of readmitted trauma patients younger than 65 years, Medicaid or Medicare patients had 2.7-fold increased odds of PPRs compared with privately insured patients. Patients of any age with congestive heart failure had 2.9 times increased odds of PPR, those with chronic obstructive pulmonary disease or complicated diabetes mellitus had 1.8 times increased odds, and those with chronic kidney disease had 1.7 times increased odds. Furthermore, as the days from discharge increased, the proportion of readmissions due to PPRs increased.

CONCLUSION

One-in-five trauma readmissions are potentially preventable, which account for more than $300 million annually in health care costs. Improved access to postdischarge ambulatory care may be key to minimizing PPRs, especially for those with certain comorbidities.

LEVEL OF EVIDENCE

Economic and value-based evaluations, level II.
Lessons from an unusual vertebrate sex-determining gene
Authors: Bertho Sylvain , Herpin Amaury , Schartl Manfred , Guiguen Yann
Published: July 2021

So far, very few sex-determining genes have been identified in vertebrates and most of them, the so-called ‘usual suspects’, evolved from genes which fulfil essential functions during sexual development and are thus already tightly linked to the process that they now govern. The single exception to this ‘usual suspects’ rule in vertebrates so far is the conserved salmonid sex-determining gene,
sdY
(sexually dimorphic on the Y chromosome), that evolved from a gene known to be involved in regulation of the immune response. It is contained in a jumping sex locus that has been transposed or translocated into different ancestral autosomes during the evolution of salmonids. This special feature of
sdY
, i.e. being inserted in a ‘jumping sex locus’, could explain how salmonid sex chromosomes remain young and undifferentiated to escape degeneration. Recent knowledge on the mechanism of action of
sdY
demonstrates that it triggers its sex-determining action by deregulating oestrogen synthesis that is a conserved and crucial pathway for ovarian differentiation in vertebrates. This result suggests that
sdY
has evolved to cope with a pre-existing sex differentiation regulatory network. Therefore, ‘limited options’ for the emergence of new master sex-determining genes could be more constrained by their need to tightly interact with a conserved sex differentiation regulatory network rather than by being themselves ‘usual suspects’, already inside this sex regulatory network.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
A neutral model for the loss of recombination on sex chromosomes
Authors: Jeffries Daniel L. , Gerchen Jörn F. , Scharmann Mathias , Pannell John R.
Published: July 2021

The loss of recombination between sex chromosomes has occurred repeatedly throughout nature, with important implications for their subsequent evolution. Explanations for this remarkable convergence have generally invoked only adaptive processes (e.g. sexually antagonistic selection); however, there is still little evidence for these hypotheses. Here we propose a model in which recombination on sex chromosomes is lost due to the neutral accumulation of sequence divergence adjacent to (and thus, in linkage disequilibrium with) the sex determiner. Importantly, we include in our model the fact that sequence divergence, in any form, reduces the probability of recombination between any two sequences. Using simulations, we show that, under certain conditions, a region of suppressed recombination arises and expands outwards from the sex-determining locus, under purely neutral processes. Further, we show that the rate and pattern of recombination loss are sensitive to the pre-existing recombination landscape of the genome and to sex differences in recombination rates, with patterns consistent with evolutionary strata emerging under some conditions. We discuss the applicability of these results to natural systems.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
A rare case of Escherichia coli and Rhizopus sinusitis complicated with pneumocephalus, E. coli psoas abscess and sepsis
Authors: Rathnayake Dulaanga , M. M. Basith , E. Tharmini , M. Umakanth , K. T. Sundaresan , Jayasekara P. I. , Sigera L. S. M. , Welagedara P. G. R. I. S. , Francis Vaithehi
Published: July 2021

Sinusitis is a common ailment a clinician comes across in their day-to-day practice. Simple as it may sound, it may become a very debilitating condition depending on the comorbidities of the patient and the organism involved. Rhizopus and

Escherichia coli

are less common organisms to affect the sinuses, but they are more common in immunocompromised patients such as patients with uncontrolled diabetes. Rhizopus can be a very debilitating infection as it erodes into the bone and blood vessels resulting in tissue necrosis. However, coinfection of both of these organisms is a very rare occurrence. Psoas abscess is also a less common infection in the immunocompetent patients but it is more common among the immunocompromised patients. It is extremely rare for both of these organisms to cause sinusitis in one patient, and for

E. coli

to simultaneously infect two different sites in the same patient. We report a case where a diabetic patient who had

E. coli

and Rhizopus coinfected sinusitis with simultaneous

E. coli

psoas abscess was successfully managed. The Rhizopus was treated with liposomal amphotericin B for 16 weeks while

E. coli

was treated with IV Meropenum. Furthermore, pneumocephalus is a condition that usually occurs following head trauma but the patient we are reporting developed pneumocephalus following Rhizopus sinusitis, which was treated with high-flow oxygen.
Facklamia lactis sp. nov., isolated from raw milk
Authors: Doll Etienne V. , Staib Lena , Huptas Christopher , Scherer Siegfried , Wenning Mareike
Published: July 2021

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus

Facklamia

but could not be assigned to any species with a validly published name.

Facklamia miroungae

ATCC BAA-466T (97.3 % 16S rRNA sequence similarity),

Facklamia languida

CCUG 37842T (96.9 %), and

Facklamia hominis

CCUG 36813T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301T and type strains of other

Facklamia

species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10–40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l−1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301T (=DSM 111018T=LMG 31861T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.
Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree
Authors: Akter Shahina , Park Jong-Hyun , Rahman M. Mizanur , Huq Md. Amdadul
Published: July 2021

A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1–0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20–37 °C, at pH 5.0–8.5 and at 0–2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus

Niastella

and was closely related to

Niastella vici

DJ57T (97.7 % similarity),

Niastella koreensis

GR20-10T (97.1 %) and

Niastella yeongjuensis

GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-29T and three closely related type strains were in the range of 78.2–83.2 % and 22.1–27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of DNA–DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29T represents a novel species within the genus

Niastella

, for which the name Niastella soli sp. nov. is proposed, with MAH-29T (=KACC 19969T=CGMCC 1.16606T) as the type strain.
Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature
Authors: Patil Prashant P. , Kumar Sanjeet , Kaur Amandeep , Midha Samriti , Bansal Kanika , Patil Prabhu B.
Published: July 2021

Stenotrophomonas maltophilia

is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 °C) is higher than environmental niches (22–30 °C). Interestingly,

S. rhizophila

a phylogenetic neighbour of

S. maltophilia

within genus

Stenotrophomonas

is unable to grow at 37 °C. Thus, it is crucial to understand how

S. maltophilia

is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis of

S. maltophilia

grown at 28 and 37 °C as temperature representative for environmental niches and the human body, respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene-expression levels at 28 and 37 °C, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 °C. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed by

S. maltophilia

during adaptation towards the human body.
Risk of Severe COVID–19 Outcomes Among Patients with Rheumatoid Arthritis in the United States
Authors: Chuo Ching-Yi , Yau Vince , Madhavan Sriraman , Tsai Larry , Chia Jenny
Published: July 2021

Introduction

Coronavirus disease 2019 (COVID–19) has infected over 22 million individuals worldwide. It remains unclear whether patients with COVID–19 and Rheumatoid Arthritis (RA) experience worse clinical outcomes compared to similar patients with COVID–19 without RA.

Aim

The aim of this study is to provide insights on how COVID–19 impacted patients with RA given the nature of the disease and medication used.

Methods

RA cases were identified via International Classification of Diseases (ICD) codes and COVID–19 cases by laboratory results in the U.S. based TriNetX network. Patients with COVID–19 and RA were propensity–score matched based on demographics with patients with COVID–19 without RA at a 1:3 ratio. A hospitalized sub-population was defined by procedure codes.

Results

We identified 1,014 COVID-19 patients with RA and 3,042 non-RA matches selected from 137,757 patients. The odds of hospitalization (non-RA:23%, RA:24.6%, OR:1.08, 95% CI: 0.88 to 1.33) or mortality (non-RA:5.4%, RA:6%, OR:0.93, 95% CI: 0.65 to 1.34) were not significantly different.

The hospitalized sub-population included 249 patients with COVID-19 and RA and 745 non-RA matches selected from 21,435 patients. The risk of intensive care unit (ICU) admission (non-RA:18.8%, RA:18.1%, OR:0.94, 95% CI: 0.60 to 1.45), and inpatient mortality (non-RA:14.4%, RA:14.5%, OR:0.86, 95% CI: 0.53 to 1.40) were not significantly different.

Conclusion

We didn’t find evidence suggesting patients with COVID–19 and RA are more likely to have severe outcomes than patients with COVID–19 without RA.

Key Messages

– Patients with Rheumatoid Arthritis (RA) tend to be older, and often have co-morbidities which could put them at greater risk of severe COVID-19 outcomes.

– This study is one of the largest studies of COVID-19 infected RA populations to date. We did not find increased risk of hospitalization, ICU admission, or mortality among RA patients vs. matched non-RA patients.

– Patients previously exposed to anti-coagulants experienced higher risks of hospitalization and overall mortality. Extra attention is needed for treating such patients.
Longitudinal changes in brain activation underlying reading fluency
Authors: Ozernov-Palchik Ola , Sury Dana , Turesky Ted K. , Yu Xi , Gaab Nadine
Published: July 2021

Reading fluency – the speed and accuracy of reading connected text – is foundational to educational success. The current longitudinal study investigates the neural correlates of fluency development using a connected-text paradigm with an individualized presentation rate. Twenty-six children completed a functional MRI task in 1st/2nd grade (time 1) and again 1-2 years later (time 2). There was a longitudinal increase in activation in the ventral occipito-temporal (vOT) cortex from time 1 to time 2. This increase was also associated with improvements in reading fluency skills and modulated by individual speed demands. These findings highlight the reciprocal relationship of the vOT region with reading proficiency and its importance for supporting the developmental transition to fluent reading. These results have implications for developing effective interventions to target increased automaticity in reading.
The Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED): Development and validation for use in pediatric populations
Authors: Puglia Meghan H. , Slobin Jacqueline S. , Williams Cabell L.
Published: July 2021

It is increasingly understood that moment-to-moment brain signal variability – traditionally modeled out of analyses as mere “noise” – serves a valuable function role and captures properties of brain function related to development, cognitive processing, and psychopathology. Multiscale entropy (MSE) – a measure of signal irregularity across temporal scales – is an increasingly popular analytic technique in human neuroscience. MSE provides insight into the time-structure and (non)linearity of fluctuations in neural activity and network dynamics, capturing the brain’s moment-to-moment complexity as it operates on multiple time scales. MSE is emerging as a powerful predictor of developmental processes and outcomes. However, differences in data preprocessing and MSE computation make it challenging to compare results across studies. Here, we (1) provide an introduction to MSE for developmental researchers, (2) demonstrate the effect of preprocessing procedures on scale-wise entropy estimates, and (3) establish a standardized EEG preprocessing and entropy estimation pipeline that generates scale-wise entropy estimates that are reliable and capable of differentiating developmental stages and cognitive states. This novel pipeline – the Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED) is fully automated, customizable, and freely available for download fromhttps://github.com/mhpuglia/APPLESEED. The dataset used herein to develop and validate the pipeline is available for download fromhttps://openneuro.org/datasets/ds003710.
Non-invasive imaging of tau-targeted probe uptake by whole brain multi-spectral optoacoustic tomography
Authors: Vagenknecht Patrick , Ono Maiko , Luzgin Artur , Ji Bin , Higuchi Makoto , Noain Daniela , Maschio Cinzia , Sobek Jens , Chen Zhenyue , Konietzko Uwe , Gerez Juan , Roland Riek , Nitsch Roger M. , Razansky Daniel , Klohs Jan , Dean-Ben Xose Luis , Ni Ruiqing
Published: July 2021

Aim

Abnormal tau accumulation plays an important role in tauopathy diseases such as Alzheimer’s disease and Frontotemporal dementia. There is a need for high-resolution imaging of tau deposits at the whole brain scale in animal models. Here, we demonstrate non-invasive whole brain imaging of tau-targeted PBB5 probe in P301L model of 4-repeat tau at 130 μm resolution using volumetric multi-spectral optoacoustic tomography (vMSOT).

Methods

The binding properties of PBB5 to 4-repeat K18 tau and Aβ42fibrils were assessed by using Thioflavin T assay and surface plasmon resonance assay. We identified the probe PBB5 suitable for vMSOT tau imaging. The imaging performance was first evaluated using postmortem human brain tissues from patients with Alzheimer’s disease, corticobasal degeneration and progressive supranuclear palsy. Concurrent vMSOT and epi-fluorescence imaging ofin vivoPBB5 targeting (i.v.) was performed in P301L and wild-type mice.Ex vivomeasurements on excised brains along with multiphoton microscopy and immunofluorescence staining of tissue sections were performed for validation. The spectrally-unmixed vMSOT data was registered with MRI atlas for volume-of-interest analysis.

Results

PBB5 showed specific binding to recombinant K18 tau fibrils, Alzheimer’s disease brain tissue homogenate by competitive binding against [11C]PBB3 and to tau deposits (AT-8 positive) in post-mortem corticobasal degeneration and progressive supranuclear palsy brain.i.v. administration of PBB5 in P301L mice led to retention of the probe in tau-laden cortex and hippocampus in contrast to wild-type animals, as also confirmed byex vivovMSOT, epi-fluorescence and multiphoton microscopy results.

Conclusion

vMSOT with PBB5 facilitates novel 3D whole brain imaging of tau in P301L animal model with high-resolution for future mechanistic studies and monitoring of putative treatments targeting tau.
Genetic similarity enhances the strength of the relationship between gut bacteria and host DNA methylation
Authors: Zhou Jia , Tesfamicael Kiflu , Zhou Shao Jia , Rollins Lee A. , Lopez Carlos M. Rodriguez
Published: July 2021

Factors such as host age, sex, diet, health status and genotype constitute the environmental envelope shaping microbial communities in the host’s gut. It has also been proposed that gut microbiota may be influenced by host epigenetics. Although the relationship between the host’s genotype/epigenotype and its associated microbiota has been the focus of a number of recent studies, the relative importance of these interactions and their biological relevance are still poorly understood. We used methylation-sensitive genotyping by sequencing to genotype and epigenotype invasive cane toads (Rhinella marina) from the species’ Australian range-core (three sites) and the invasion-front (three sites), and 16S rRNA gene sequencing to characterize their gut bacterial communities. We tested the effect of host genotype and epigenotype (i.e., methylome) on gut bacterial communities. Our results indicate that the genotypes, epigenotypes and gut communities of the range-core and invasion-front are significantly different from one another. We found a positive association between host pairwise genetic and epigenetic distances. More importantly, a positive relationship was found between the host’s epigenetic and gut bacterial pairwise distances. Interestingly, this association was stronger in individuals with low genetic differentiation. Our findings suggest that in range-expanding populations, where individuals are often genetically similar, the interaction between gut bacterial communities and host methylome may provide a mechanism through which invaders increase the plasticity of their response to novel environments, potentially increasing their invasion success.
Application of stable isotopes to study movement ecology and diet variation in a migratory songbird
Authors: Contina Andrea , Pierce Allison K. , Yanco Scott W. , Bridge Eli S. , Kelly Jeffrey F. , Wunder Michael B.
Published: July 2021

Whether and how migratory organisms exhibit inter-individual behavioral and/or physiological variation across movement strategies remains an open question. The Dark-eyed Junco (Junco hyemalis) is a migratory songbird known for its intra-species variation displayed in relation to morphology, song repertoires, and migration. Thus, studies focusing on juncos can reveal how migratory strategy may covary with other individual-scale factors and, therefore, identify the selective forces driving intra-species variations throughout its distribution. We used Dark-eyed Junco hydrogen stable isotope feather values (delta2H) and implemented a Bayesian framework to infer the breeding and molting origin of migratory juncos captured on their winter grounds in Oklahoma, United States (U.S.). We modeled the distribution of feather hydrogen stable isotope values as a function of five morphological variables including body mass and fat deposition measured in Oklahoma during the winter. We then investigated the trade-off between longer and more energetically costly migration strategies in relation to diet preferences through carbon (delta13C) and nitrogen (delta15N) stable isotope analysis from feather values. Dark-eyed Juncos wintering in south central U.S. likely originate from multiple breeding populations in northern U.S. and Canada. Body condition at the wintering ground (e.g., mass) had no effect on feather hydrogen stable isotope abundance. However, we found a positive correlation between nitrogen and hydrogen stable isotopes, suggesting that a trophic level shift towards insect consumption might occur in individuals migrating from southern latitudes. Increased insect-derived protein consumption might be explained by reduced fatty-acid reserves necessary to complete a shorter migratory journey.
Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration
Authors: Souto-Maior Caetano , Serrano Negron Yazmin L. , Harbison Susan T.
Published: July 2021

All but the simplest phenotypes are believed to result from interactions between two or more genes forming complex networks of gene regulation. Sleep is a complex trait known to depend on the system of feedback loops of the circadian clock, and on many other genes; however, the main components regulating the phenotype and how they interact remain an unsolved puzzle. Genomic and transcriptomic data may well provide part of the answer, but a full account requires a suitable quantitative framework. Here we conducted an artificial selection experiment for sleep duration with RNA-seq data acquired each generation. The phenotypic results are robust across replicates and previous experiments, and the transcription data provides a high-resolution, time-course data set for the evolution of sleep-related gene expression. In addition to a Hierarchical Generalized Linear Model analysis of differential expression that accounts for experimental replicates we develop a flexible Gaussian Process model that estimates interactions between genes. 145 gene pairs are found to have interactions that are different from controls. Our method appears to be not only more specific than standard correlation metrics but also more sensitive, finding correlations not significant by other methods. Statistical predictions were compared to experimental data from public databases on gene interactions. Mutations of candidate genes implicated by our results affected night sleep, and gene expression profiles largely met predicted gene-gene interactions.
Distributed and multifaceted effects of threat and safety
Authors: Morrow Kelly , Dinavahi Murty , Kim Jongwan , Song Song-tao , Hu Kesong , Pessoa Luiz
Published: July 2021

Sustained anticipation of unpredictable aversive events generates anticipatory processing that is central to anxiety. In the present functional Magnetic Resonance Study (fMRI) study, we examined how sustained threat is processed in the human brain. We used a relatively large sample (N= 109) and employed a Bayesian multilevel analysis approach to contrastthreatandsafeperiods. Our analyses demonstrated that the effect of sustained threat is heterogeneous and distributed across the brain. Thus, the impact of threat is widespread, and not restricted to a small set of putatively emotion-related regions, such as the amygdala and the bed nucleus of the stria terminalis. Both transient and sustained, and increased and decreased responses during threat were observed. Our study reveals that transitioning between threat and safe states, and vice versa, leads to a widespread switch in brain responding that involves most of the brain.
Novel insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis
Authors: Uehara Yasuaki , Nikolaidis Nikolaos M. , Pitstick Lori B. , Wu Huixing , Yu Jane J. , Zhang Erik , Hasegawa Yoshihiro , Tanaka Yusuke , Noel John G. , Gardner Jason C. , Kopras Elizabeth J. , Haffey Wendy D. , Greis Kenneth D. , Guo Jinbang , Woods Jason C. , Wikenheiser-Brokamp Kathryn A. , Zhao Shuyang , Xu Yan , Kyle Jennifer E. , Ansong Charles , Teitelbaum Steven L. , Inoue Yoshikazu , Altinişik Göksel , McCormack Francis X.
Published: July 2021

Pulmonary alveolar microlithiasis (PAM) is an autosomal recessive lung disease caused by a deficiency in the pulmonary epithelial Npt2b sodium-phosphate co-transporter that results in accumulation of phosphate and formation of hydroxyapatite microliths in the alveolar space. The single cell transcriptomic analysis of a PAM lung explant showing a robust osteoclast gene signature in alveolar monocytes and the finding that calcium phosphate microliths contain a rich protein and lipid matrix that includes bone resorbing osteoclast enzymes suggested a role for osteoclast-like cells in the defense against microliths. While investigating the mechanisms of microlith clearance, we found that Npt2b modulates pulmonary phosphate homeostasis through effects on alternative phosphate transporter activity and alveolar osteoprotegerin, and that microliths induce osteoclast formation and activity in a receptor activator of nuclear factor-κB ligand (RANKL) and dietary phosphate dependent manner. This work reveals that Npt2b and pulmonary osteoclast-like cells play key roles in pulmonary homeostasis and suggest potential new therapeutic targets for the treatment of lung disease.
Environmental assessment of entropy control in flight process
Authors: Sogut Mehmet Ziya
Published: July 2021

Purpose

This study aims to examine exergy efficiency of engines and entropy performances at the flight process. In addition, the improvements that can be achieved in the system with the effective parametric controls of the engine have been evaluated in terms of both efficiency and entropy in the system.

Design/methodology/approach

According to the flight characteristics of the engine, the altitude-dependent irreversibilities and their environmental effects were discussed with two developed indicators, energy performance indicator (EPI) and sustainability indicator (SI).

Findings

According to the results of both indicators, the energy efficiency potential of the engine during the flight process was found to be 15.02%, while the fuel-based efficiency potential was 18.84%.

Research limitations/implications

It is limited by the flight process of a Turboprop engine.

Practical implications

The management tools and criteria of entropy are very difficult model studies. The study offers an evaluable approach based on two basic criteria developed for engines.

Social implications

In monitoring and review of entropy management related to fossil fuel technologies, key indicators developed can be used as benchmarks for managing emission sources

Originality/value

The two basic indicators developed can be used as monitoring measurement tools of sustainable energy and environmental performances for engines and applications.
Multi-objective structural optimization of a wind turbine blade using NSGA-II algorithm and FSI
Authors: Özkan Ramazan , Genç Mustafa Serdar
Published: July 2021

Purpose

Wind turbines are one of the best candidates to solve the problem of increasing energy demand in the world. The aim of this paper is to apply a multi-objective structural optimization study to a Phase II wind turbine blade produced by the National Renewable Energy Laboratory to obtain a more efficient small-scale wind turbine.

Design/methodology/approach

To solve this structural optimization problem, a new Non-Dominated Sorting Genetic Algorithm (NSGA-II) was performed. In the optimization study, the objective function was on minimization of mass and cost of the blade, and design parameters were composite material type and spar cap layer number. Design constraints were deformation, strain, stress, natural frequency and failure criteria. ANSYS Composite PrepPost (ACP) module was used to model the composite materials of the blade. Moreover, fluid–structure interaction (FSI) model in ANSYS was used to carry out flow and structural analysis on the blade.

Findings

As a result, a new original blade was designed using the multi-objective structural optimization study which has been adapted for aerodynamic optimization, the NSGA-II algorithm and FSI. The mass of three selected optimized blades using carbon composite decreased as much as 6.6%, 11.9% and 14.3%, respectively, while their costs increased by 23.1%, 29.9% and 38.3%. This multi-objective structural optimization-based study indicates that the composite configuration of the blade could be altered to reach the desired weight and cost for production.

Originality/value

ACP module is a novel and advanced composite modeling technique. This study is a novel study to present the NSGA-II algorithm, which has been adapted for aerodynamic optimization, together with the FSI. Unlike other studies, complex composite layup, fiber directions and layer orientations were defined by using the ACP module, and the composite blade analyzed both aerodynamic pressure and structural design using ACP and FSI modules together.