bluuebunny/crossref_metadata_2025 huggingface dataset:
Anisakiasis in Palatine Tonsil
Authors: Cha Eun Joo , Kim Jung Soo , Heo Sung Jae
Published: February 2022

Anisakiasis is a parasitic infection caused by ingesting raw or undercooked fish and seafood infected with Anisakis larvae. Anisakis genus is mostly found in the mucosal or submucosal layer of the stomach and intestine. However, the reports of anisakiasis in tonsils are highly uncommon. A 54-year-old woman with clinical features of sore throat and foreign-body sensation for 10 days after eating raw and undercooked fish. A wriggling worm was noted beneath the mucosa of the right palatine tonsil upon endoscopic examination. The worm was immediately removed completely and histological examination revealed anisakiasis. Reports of anisakia-sis in the tonsils are scarce, but it should be considered at the initial physical examination of patients who visit the hospital for sore throat after eating raw fish. We report a case of anisakiasis in the palatine tonsils, which to date has been rarely reported in the literature.
Association between Surgery, Anesthesia, and Obstetric Workforce and Emergent Surgical and Obstetric Mortality among United States Hospital Referral Regions
Authors: Truche Paul , Semco Robert S. , Hansen Nathaniel F. , Uribe-Leitz Tarsicio , Roa Lina , Allar Benjamin G. , Layman Ilan B. , Bergmark Regan W. , Williams Wendy , Riviello Robert , McClain Craig D. , Jarman Molly P. , Cooper Zara , Meara John G. , Ortega Gezzer
Published: February 2022

Objective:

To determine the association between SAO workforce and mortality from emergent surgical and obstetric conditions within US HR Rs.

Background:

SAO workforce per capita has been identified as a core metric of surgical capacity by the Lancet Commission on Global Surgery, but its utility has not been assessed at the subnational level for a high-income country.

Methods:

The number of practicing surgeons, anesthesiologists, and obstetricians per capita was estimated for all HRRs using the US Health Resources & Services Administration Area Health Resource File Database. Deaths due to emergent general surgical and obstetric conditions were determined from the Center for Disease Control and Prevention WONDER database. We utilized B-spline quantile regression to model the relationship between SAO workforce and emergent surgical mortality at different quantiles of mortality and calculated the expected change in mortality associated with increases in SAO workforce.

Results:

The median SAO workforce across all HRRs was 74.2 per 100,000 population (interquartile range 33.3-241.0). All HRRs met the Lancet Commission on Global Surgery lower target of 20 SAO per 100,000, and 97.7% met the upper target of 40 per 100,000. Nearly 2.8 million Americans lived in HRRs with fewer than 40 SAO per 100,000. Increases in SAO workforce were associated with decreases in surgical mortality in HRRs with high mortality, with minimal additional decreases in mortality above 60 to 80 SAO per 100,000.

Conclusions:

Increasing SAO workforce capacity may reduce emergent surgical and obstetric mortality in regions with high surgical mortality but diminishing returns may be seen above 60 to 80 SAO per 100,000. Trial Registration: N/A
The costs and benefits of dispersal in small populations
Authors: Polechová Jitka
Published: February 2022

Dispersal has three major effects on adaptation. First, gene flow mixes alleles adapted to different environments, potentially hindering (swamping) adaptation. Second, it brings in other variants and inflates genetic variance: this aids adaptation to spatially (and temporally) varying environments but if selection is hard, it lowers the mean fitness of the population. Third, neighbourhood size, which determines how weak genetic drift is, increases with dispersal—when genetic drift is strong, increase of the neighbourhood size with dispersal aids adaptation. In this note, I focus on the role of dispersal in environments that change gradually across space, and when local populations are quite small such that genetic drift has a significant effect. Using individual-based simulations, I show that in small populations, even leptokurtic dispersal benefits adaptation by reducing the power of genetic drift. This has implications for management of fragmented or marginal populations: the beneficial effect of increased dispersal into small populations is stronger than swamping of adaption under a broad range of conditions, including a mixture of local and long-distance dispersal. However, when environmental gradient is steep, heavily fat-tailed dispersal will swamp continuous adaptation so that only patches of locally adapted subpopulations remain.

This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.
Environmental variation and biotic interactions limit adaptation at ecological margins: lessons from rainforestDrosophilaand European butterflies
Authors: O'Brien Eleanor K. , Walter Greg M. , Bridle Jon
Published: February 2022

Models of local adaptation to spatially varying selection predict that maximum rates of evolution are determined by the interaction between increased adaptive potential owing to increased genetic variation, and the cost genetic variation brings by reducing population fitness. We discuss existing and new results from our laboratory assays and field transplants of rainforestDrosophilaand UK butterflies along environmental gradients, which try to test these predictions in natural populations. Our data suggest that: (i) local adaptation along ecological gradients is not consistently observed in time and space, especially where biotic and abiotic interactions affect both gradient steepness and genetic variation in fitness; (ii) genetic variation in fitness observed in the laboratory is only sometimes visible to selection in the field, suggesting that demographic costs can remain high without increasing adaptive potential; and (iii) antagonistic interactions between species reduce local productivity, especially at ecological margins. Such antagonistic interactions steepen gradients and may increase the cost of adaptation by increasing its dimensionality. However, where biotic interactions do evolve, rapid range expansion can follow. Future research should test how the environmental sensitivity of genotypes determines their ecological exposure, and its effects on genetic variation in fitness, to predict the probability of evolutionary rescue at ecological margins.

This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.
Climate-driven variation in biotic interactions provides a narrow and variable window of opportunity for an insect herbivore at its ecological margin
Authors: Stewart James E. , Maclean Ilya M. D. , Trujillo Gara , Bridle Jon , Wilson Robert J.
Published: February 2022

Climate-driven geographic range shifts have been associated with transitions between dietary specialism and generalism at range margins. The mechanisms underpinning these often transient niche breadth modifications are poorly known, but utilization of novel resources likely depends on phenological synchrony between the consumer and resource. We use a climate-driven range and host shift by the butterflyAricia agestisto test how climate-driven changes in host phenology and condition affect phenological synchrony, and consider implications for host use. Our data suggest that the perennial plant that was the primary host before range expansion is a more reliable resource than the annual Geraniaceae upon which the butterfly has become specialized in newly colonized parts of its range. In particular, climate-driven phenological variation in the novel hostGeranium dissectumgenerates a narrow and variable ‘window of opportunity' for larval productivity in summer. Therefore, although climatic change may allow species to shift hosts and colonise novel environments, specialization on phenologically limited hosts may not persist at ecological margins as climate change continues. We highlight the potential role for phenological (a)synchrony in determining lability of consumer–resource associations at range margins and the importance of considering causes of synchrony in biotic interactions when predicting range shifts.

This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.
Streptomyces corallincola and Kineosporia corallincola sp. nov., two new coral-derived marine actinobacteria
Authors: Buangrab Kusuma , Sutthacheep Makamas , Yeemin Thamasak , Harunari Enjuro , Igarashi Yasuhiro , Sripreechasak Paranee , Kanchanasin Pawina , Tanasupawat Somboon , Phongsopitanun Wongsakorn
Published: February 2022

Two new marine actinobacteria, designated as J2-1T and J2-2T, were isolated from a coral, Favites pentagona, collected from Rayong Province, Thailand. The taxonomic positions of the two strains were identified based on polyphasic taxonomy. Based on morphological characteristics and chemotaxonomy, strains J2-1T and J2-2T were identified as members of the genus

Streptomyces

and

Kineosporia

, respectively. Strains J2-1T and J2-2T showed the highest 16S rRNA gene sequence similarity to

Streptomyces broussonetiae

T44T (98.62 %) and

Kineosporia babensis

VN05A0415T (98.08 %), respectively. Strain J2-1T had chemotaxonomic properties resembling members of the genus

Streptomyces

. ll-Diaminopimelic acid, glucose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, unidentified aminolipid and five unidentified phospholipids were detected as the polar lipids. The major cellular fatty acids were C16 : 0 iso, C15 : 0 anteiso, C15 : 0 iso, C16 : 0, C17 : 0 anteiso, C14 : 0 iso and C17 : 0 iso. Strain J2-2T a showed similar cell composition to members of the genus

Kineosporia

. Both isomers of ll- and meso-diaminopimelic acid were detected in the peptidoglycan. Arabinose, galactose, madurose and xylose were observed in the whole-cell hydrolysate. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylcholine, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were C16 : 0, C18 : 1 ω9c, C18 : 0 10-methyl, tuberculostearic acid, C18 : 0 and C17 : 0. Both strains could be distinguished from their closely related type strains according to their phenotypic characteristics. Comparative genome analysis indicated the delineation of two novel species based on digital DNA–DNA hybridization and average nucleotide identity values, which were below 70 and 95 %, respectively. The names proposed are Streptomyces corallincola sp. nov. (J2-1T=TBRC 13503T=NBRC 115066T) and Kineosporia corallincola sp. nov. (J2-2T=TBRC 13504T=NBRC 114885T).
Clostridium thailandense sp. nov., a novel CO2-reducing acetogenic bacterium isolated from peatland soil
Authors: Chaikitkaew Srisuda , In-chan Supattra , Singkhala Apinya , Tukanghan Wisarut , Mamimin Chonticha , Reungsang Alissara , Birkeland Nils-Kåre , O-Thong Sompong
Published: February 2022

Some species of the genus

Clostridium

are efficient acetate producers and have been deemed useful for upgrading industrial biogas. An acetogenic, strictly anaerobic, Gram-stain-positive, subterminal endospore-forming bacterium designated strain PL3T was isolated from peatland soil enrichments with H2 and CO2. Cells of strain PL3T were 0.8–1.0×4.0–10.0 µm in size and rod-shaped. Growth of strain PL3T occurred at pH 6.0–7.5 (optimum, pH 7.0), at 20–40 °C (optimum, 30 °C) and with 0–1.5 % (w/v) NaCl (optimum, 0.5%). Biochemical analyses revealed that strain PL3T metabolized lactose, maltose, raffinose, rhamnose, lactic acid, sorbitol, arabinose and glycerol. Acetic acid was the predominant metabolite under anaerobic respiration with H2/CO2. The major cellular fatty acids were C16 : 0, C16 : 1
cis 9 and C17 : 0 cyc. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, aminolipid and aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PL3T belongs to the genus

Clostridium

with the highest sequence similarity to

Clostridium aciditolerans

DSM 17425T (98.6 %) followed by

Clostridium nitrophenolicum

(97.8 %). The genomic DNA G+C content of strain PL3T was 31.1 mol%.The genomic in silico DNA–DNA hybridization value between strain PL3T and

C. aciditolerans

DSM 17425T was 25.1 %, with an average nucleotide identity of 80.2 %. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PL3T was suggested to represent a novel species of the genus

Clostridium

, for which the name Clostridium thailandense sp. nov. is proposed. The type strain is PL3T (=DSM 111812T=TISTR 2984T).
Can we see gender through the microscope? The research output using menstrual blood cells has much to say
Authors: Manica Daniela Tonelli , Asensi Karina Dutra , Mazzarelli Gaia , Barata Germana , Goldenberg Regina Coeli dos Santos
Published: February 2022

Despite proven scientific quality of menstrual blood mesenchymal cells, research and science output using those cells is still incipient and considered taboo. This study analyzes the literature of the menstrual blood mesenchymal stromal/stem cells (mbMSC) at PubMed database between (2008 – 2020) and the social attention it received on Twitter. A comparative analysis showed that mbMSC has a very small space within mesenchymal cells research (0.25%). Most first authors are women (53.2%), whereas most last authors are men (63.74%). Menstrual blood tends to be less used in experiments and its scientific value tends to be underestimated, which brings gender bias to a technical and molecular level. Although women are more positive in the mbMSC debate on Twitter, communication efforts toward visibility and public interest in menstrual cells has room to grow.
Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery
Authors: Zhang Xiaolei , Theotokis Pantazis I. , Li Nicholas ,   the SHaRe Investigators, Wright Caroline F. , Samocha Kaitlin E. , Whiffin Nicola , Ware James S.
Published: February 2022

The clinical impact of most germline missense variants in humans remains unknown. Genetic constraint identifies genomic regions under negative selection, where variations likely have functional impacts, but the spatial resolution of existing constraint metrics is limited. Here we present the Homologous Missense Constraint (HMC) score, which measures genetic constraint at quasi single amino-acid resolution by aggregating signals across protein homologues. We identify one million possible missense variants under strong negative selection. HMC precisely distinguishes pathogenic variants from benign variants for both early-onset and adult-onset disorders. It outperforms existing constraint metrics and pathogenicity meta-predictors in prioritising de novo mutations from probands with developmental disorders (DD), and is orthogonal to these, adding power when used in combination. We demonstrate utility for gene discovery by identifying seven genes newly-significant associated with DD that could act through an altered-function mechanism. Overall, HMC is a novel and strong predictor to improve missense variant interpretation.
Genomic monitoring unveils a high prevalence of SARS-CoV-2 Omicron variant in vaccine breakthrough cases
Authors: Campos Gúbio Soares , Giovanetti Marta , de Moraes Laise , da Hora Helena Souza , de Alcantara Keila Oliveira Motta , Sardi Silvia Ines
Published: February 2022

Genome sequencing proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by SARS-CoV-2, i.e., coronavirus disease (COVID-19). Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern (VOCs). To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different VOCs in these cases. Nasopharyngeal swabs from infected (symptomatic and asymptomatic), fully vaccinated individuals (n=29) who were of varying age and had RT-qPCR Ct values of ≤30 were subjected to viral sequencing using Nanopore technology. Our analysis revealed that the Omicron variant was found in 99% of cases and that only one case was due to the Delta variant. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of VOCs not neutralized by the vaccines.
SARS-CoV-2 antibody persistence after five and twelve months: A cohort study from South-Eastern Norway
Authors: Sarjomaa Marjut , Diep Lien My , Zhang Chi , Tveten Yngvar , Reiso Harald , Thilesen Carina , Nordbø Svein Arne , Berg Kristine Karlsrud , Aaberge Ingeborg , Pearce Neil , Kersten Hege , Vandenbroucke Jan Paul , Eikeland Randi , Møller Fell Anne Kristin
Published: February 2022

Objectives

To assess total antibody levels against Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2) spike protein up to 12 months after Coronavirus Disease (COVID-19) infection in non-vaccinated individuals and the possible predictors of antibody persistence.

Methods

This is a prospective multi-centre longitudinal cohort study.

Participants

The study included SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) positive and negative participants in South-Eastern Norway from February to December 2020. Possible predictors of SARS-CoV-2 total antibody persistence was assessed. The SARS-CoV-2 total antibody levels against spike protein were measured three to five months after PCR in 391 PCR-positive and 703 PCR-negative participants; 212 PCR-positive participants were included in follow-up measurements at 10 to 12 months. The participants completed a questionnaire including information about symptoms, comorbidities, allergies, body mass index (BMI), and hospitalisation.

Primary outcome

The SARS-CoV-2 total antibody levels against spike protein three to five and 10 to 12 months after PCR positive tests.

Results

SARS-CoV-2 total antibodies against spike protein were present in 366 (94%) non-vaccinated PCR-positive participants after three to five months, compared with nine (1%) PCR-negative participants. After 10 to 12 months, antibodies were present in 204 (96%) non-vaccinated PCR-positive participants. Of the PCR-positive participants, 369 (94%) were not hospitalised. The mean age of the PCR-positive participants was 48 years (SD 15, range 20-85) and 50% of them were male. BMI ≥ 25 kg/m2 was positively associated with decreased antibody levels (OR 2.34, 95% CI 1.06 to 5.42). Participants with higher age and self-reported initial fever with chills or sweating were less likely to have decreased antibody levels (age: OR 0.97, 95% CI 0.94 to 0.99; fever: OR 0.33, 95% CI 0.13 to 0.75).

Conclusion

Our results indicate that the level of SARS-CoV-2 total antibodies against spike protein persists for the vast majority of non-vaccinated PCR-positive persons at least 10 to 12 months after mild COVID-19.
The validity and reliability of parent’s recall for routine Immunization in Cameroon: an evaluative study
Authors: Yakum Martin Ndinakie , Funwie Atanga Desmond , Ajong Atem Bethel , Shah Zahir
Published: February 2022

Introduction

In the absence of immunization documentations, parent’s recall is used to assess children immunization status. During the 2018 demograhpic and health survey in Cameroon, parent’s recall was the only source of information for 47% of chidren assessed for immunization coverage. The objective of this study was to determine the validity of parent’s recall for immunization using the vaccination card as the reference in Yaounde-Cameroon.

Methods

The study targeting parents of children aged 0-59months who had their children’s vaccination cards. The immunization history of each child was taken based on both parent’s recall and vaccination card. Using the vaccination card as a reference, the sensitivity, specificity, positive predictive value and negative predictive value of parent’s recall were calculated. The degree of agreement and the kappa statistics between the two methods were calculated using R version 4.1.0 (2021-05-18).

Results

A total of 529 households were visited and 87 elligible parents enrolled. Approximately 55.2% of the children were girls and 53% of them were aged 12-59 months. In total, 94.25% of the participants enrolled were one of the biological parents of the children, with mothers making the majority 86.20% of participants. When combined for all vaccines in the EPI (i.e. one dose BCG, 4 doses of OPV, 3 doses of pentavalent vaccine, 3 doses of PCV-13, 2 doses of rotavirus vaccine, one dose of measles/rubella vaccine and one dose of the yellow fever vaccine), the sensitivity, specificity, positive predictive value, and negative predictive value of parent’s recall were 63%, 60%, 90%, and 23% respectively. The degree of agreement between the two sources was highest for BCG(94%) and lowest with Polio2(32%). Parent’s recall(94%) was most likely to correctly predict BCG vaccination status of a child than using the scars on the forarm(74%).

Conclusion

Our conclusion is that validity and reliability of parent’s recall vary a lot across different vaccines and parent’s recall is not very reliable for immunization status assessment in children. Parent’s recall is preferred for verifying BCG immunization to scars on the forarm. In general, we recommend that parent’s recall for routine immunization should be used only as a last resort or for BCG, and measles and Yellow Fever vaccines.
The burden of vaccine hesitancy for routine immunization in Yaounde-Cameroon: restrictive sampling technique
Authors: Yakum Martin Ndinakie , Funwie Atanga D , Ajong Atem Bethel , Tsafack Marcelin , Ze Linda Evans Eba , Shah Zahir
Published: February 2022

Immunization is the most cost-effective health intervention in the world yet, vaccination uptake is still low with less than 50% of children aged 12-23 months fully vaccinated Cameroon. The objective of this study was to estimate the burden of vaccine hesitancy associated with routine EPI vaccines in Yaounde-Cameroon. A two-stage cross-sectional cluster survey was conducted in Yaoundé in May-June 2022, targeting parents/guardians of children 0-59 months. Clusters were selected with probability proportionate to size (PPS) and household’s selection done using a restricted sampling method. Data collection was done using an interviewer-administered questionnaire. Data were cleaned using MS-Excel 2019, and analyzed with R version 4.1.0 (2021-05-18). A total of 529 participants were enrolled out of 708 visited, giving a non-response rate of 25%. In total, vaccine hesitancy was reported in 137(25.90[22.35-29.80] %), and vaccine hesitancy prevalence did not vary significantly across different households’ wealth levels (p-value= 0.3786). However, in wealthy households’ refusal of vaccines (14%) was less than in poorer households (20%). Lack of trust, confidence, and perceived complacency are the leading causes of vaccine hesitancy related to routine immunization in Yaounde-Cameroon. We, therefore, recommend that the burden of vaccine hesitancy should be assessed at national scale and identify sources of misinformation that are at the origin of vaccine hesitancy. Having a clear notion of the effect of social media(Facebook, Instagram, WhatsApp, etc,), radio, TV, and other information sources might guide interventions to combat vaccine hesitancy.
Knowledge, Attitude and Perceptions Regarding Male Infertility among the Medical Students and Healthcare Professionals of Bangladesh
Authors: Iktidar Mohammad Azmain , Khairul Islam A M , Chowdhury Sreshtha , Roy Simanta , Islam Mahzabeen , Chowdhury Tonmoy , Tabassum Mustari Nailah , Ali Tahsin Sumat , Akash Atandra , Ahmed Mashrur , Zafar Faraz Al , Hawlader Mohammad Delwer Hossain
Published: February 2022

Background

People worldwide have many misconceptions regarding reproductive health and fertility because infertility is still a taboo subject. The general public seek medical and psychological counsel and assistance from health experts about male infertility. Therefore, this study aimed to explore the knowledge, attitude, and behavior regarding male infertility among medical students and health care workers of Bangladesh.

Method

This cross-sectional study used quota sampling to assure equal participation from each of the eight divisions of Bangladesh and convenience. 46 structured questions were used to assess respondents’ knowledge, attitudes, and perceptions (34-items for knowledge, 5-items for attitudes, and 7-items for perceptions).Two scoring systems were employed with the mean scores as cut-off value for good knowledge and positive attitude. The mean knowledge and attitude scores were then correlated with sociodemographic factors using chi-square and two-independent sample t-tests. Finally, we performed binary logistic regression to explore predictors of good knowledge and positive attitude.

Result

Among the participant, 49.82% did not have a good male infertility knowledge and nearly 60.79% had negative attitudes regarding male infertility. Young (23-26 years) healthcare professionals and medical students were more likely to have good knowledge than others (OR: 1.81; 95% CI: 1.099 to 2.988). Surprisingly, females were more likely to have positive attitude (OR=1.48; 95%CI: 1.002 and 2.19, p=0.049) compared to males. Among all the professions, MBBS doctors were most likely to have good knowledge and positive attitude regarding male infertility. Good knowledge of male infertility predicted positive attitude (OR=1.61; 95% CI: 1.105 and 2.346, p=0.013) and vice versa.

Conclusion

Our research found that despite favourable opinions, healthcare professionals and medical students in Bangladesh had inadequate knowledge and negative attitudes regarding male infertility. This emphasizes the need for interdisciplinary training programs, standardization of healthcare worker guidelines, and curricular adjustments for medical students.
Wastewater surveillance using ddPCR reveals highly accurate tracking of Omicron variant due to altered N1 probe binding efficiency
Authors: Schussman Melissa K. , Roguet Adelaide , Schmoldt Angela , Dinan Brooke , McLellan Sandra L.
Published: February 2022

Wastewater surveillance for SARS-CoV-2 is being used worldwide to understand COVID-19 infection trends in a community. We found the emergence and rapid timeline for dominance of the Omicron variant was accurately reflected in wastewater when measured with droplet digital (dd)PCR. We were able to distinguish Omicron from the circulating Delta variant because Omicron has a mutation in the N1 probe binding region that diminished the fluorescent signal within individual droplets. The ddPCR platform may be advantageous for wastewater surveillance since analysis of the data can segregate fluorescent signals from different individual templates. In contrast, platforms such as qPCR that rely solely on the intensity of fluorescence for quantification would not distinguish a subset of variants with mutations affecting the reaction and could underestimate SARS-CoV-2 concentrations. The proportion of Omicron in wastewater was tightly correlated to clinical cases in five cities and provided a higher resolution timeline of appearance and dominance (>75%) than sequenced clinical samples, which were limited in less populated areas. Taken together, this work demonstrates wastewater is a reliable metric for tracking SARS-CoV-2 at a population level.
Spontaneous behavioural recovery following stroke relates to the integrity of sensory and association cortices
Authors: Nashed Joseph Y. , Shearer Kaden T. , Wang Justin Z. , Chen Yining , Cook Elise E. , Champagne Allen A. , Coverdale Nicole S. , Fernandez-Ruiz Juan , Striver Shirley I. , Gallivan Jason P. , Cook Douglas J.
Published: February 2022

Stroke is a devastating disease that results in neurological deficits and represents a leading cause of death and disability worldwide. Following a stroke, there is a degree of spontaneous recovery of function, the neural basis of which is of great interest among clinicians in their efforts to reduce disability following stroke and enhance rehabilitation. Conventionally, work on spontaneous recovery has tended to focus on the neural reorganization of motor cortical regions, with comparably little attention being paid to changes in non-motor regions and how these relate to recovery. Here we show, using structural neuroimaging in a macaque stroke model and by exploiting individual differences in spontaneous behavioural recovery, that the preservation of regions in the sensory and association cortices predict animal recovery. To characterize recovery, we performed a clustering analysis using Non-Human Primate Stroke Scale (NHPSS) scores and identified a good versus poor recovery group. By comparing the preservation of brain volumes in the two groups, we found that brain areas in integrity of brain areas in parietal, temporal and somatosensory cortex were associated with better recovery. In addition, a decoding approach performed across all subjects revealed that the preservation of specific brain regions in the parietal, somatosensory and medial frontal cortex predicted recovery. Together, these findings highlight the importance of the sensory and association regions in spontaneous behavioural recovery, supporting the notion that the ‘sensory retraining’ of impairments following stroke is critical to recovery and motor function.
Combined single-cell RNA-seq profiling and enhancer editing reveals critical spatiotemporal controls over thalamic nuclei formation in the murine embryo
Authors: Govek Kiya W. , Chen Sixing , Sgourdou Paraskevi , Yao Yao , Woodhouse Steven , Chen Tingfang , Fuccillo Marc V. , Epstein Douglas J. , Camara Pablo G.
Published: February 2022

The thalamus is the principal information hub of the vertebrate brain, with essential roles in sensory and motor information processing, attention, and memory. The molecular mechanisms regulating the formation of thalamic nuclei are unclear. We apply longitudinal single-cell RNA-sequencing, regional abrogation of Sonic-hedgehog (Shh), and spatial profiling of gene expression to map the developmental trajectories of thalamic progenitors, intermediate progenitors, and post-mitotic neurons as they coalesce into distinct thalamic nuclei. These data reveal that the complex architecture of the thalamus is established early during embryonic brain development through the coordinated action of four cell differentiation lineages derived from Shh-dependent and independent progenitors. We systematically characterize the gene expression programs that define these lineages across time and demonstrate how their disruption upon Shh depletion causes pronounced locomotor impairment resembling infantile Parkinson’s disease. These results reveal key principles of thalamic development and provide mechanistic insights into neurodevelopmental disorders resulting from thalamic dysfunction.
A conditional survival distribution-based method for censored data imputation: overcoming the hurdle in machine learning-based survival analysis
Authors: Wang Yizhuo , Flowers Christopher R. , Li Ziyi , Huang Xuelin
Published: February 2022

Data analyses by machine learning (ML) algorithms are gaining popularity in biomedical research. When time-to-event data are of interest, censoring is common and needs to be properly addressed. Most ML methods cannot conveniently and appropriately take the censoring information into consideration, potentially leading to inaccurate or biased results. We aim to develop a general-purpose method for imputing censored survival data, facilitating downstream ML analysis. In this study, we propose a novel method of imputing the survival times for censored observations. The proposal is based on their conditional survival distributions (CondiS) derived from Kaplan-Meier estimators. CondiS can replace censored observations with their best approximations from the statistical model, allowing for direct application of ML methods. When covariates are available, we extend CondiS by incorporating the covariate information through ML modeling (CondiS-X), which further improves the accuracy of the imputed survival time. Compared with existing methods with similar purposes, the proposed methods achieved smaller prediction errors and higher concordance with the underlying true survival times in extensive simulation studies. We also demonstrated the usage and advantages of the proposed methods through two real-world cancer datasets. The major advantage of CondiS is that it allows for the direct application of standard ML techniques for analysis once the censored survival times are imputed. We present a user-friendly R package to implement our method, which is a useful tool for ML-based biomedical research in this era of big data.
Four doses of the inactivated SARS-CoV-2 vaccine redistribute humoral immune responses away from the Receptor Binding Domain
Authors: Wang Ji , Deng Caiguangxi , Liu Ming , Liu Yihao , Li Liubing , Huang Zhangping , Shang Liru , Jiang Juan , Li Yongyong , Mo Ruohui , Zhang Hui , Liu Min , Peng Sui , Xiao Haipeng
Published: February 2022

A recent MMWR reported that the effectiveness of a 3rd dose of SARS-CoV-2 mRNA vaccine waned quickly in the Omicron-predominant period. Similarly, a substantial decline of immune responses induced by a 3rd dose of inactivated vaccines was also observed in our study. In response to the fast waning immune response and the great threat of Omicron variant of concern (VOC) to frontline healthcare workers (HCWs), 38 HCWs who were in our previous cohort investigating responses to the first three doses of inactivated vaccines participated in the current study and volunteered to receive a 4th homologous booster. Here, we demonstrated that the 4th dose is safe and capable of recalling waned immune responses 6 months after the 3rd dose. However, a greater suppression on the induction of overall Neutralizing antibodies (NAbs) and NAbs targeting the receptor-binding domain (RBD) was found in participants with stronger immune responses after the 3rd dose. As a result, a stepwise elevation of RBD-NAbs from the 1st to the 3rd vaccination achieved a “turning point”. The peak RBD-NAbs level induced by the 4th dose was inferior to the peak of the 3rd dose. Accompanied with reduced induction of RBD-NAbs, the immune system shifted responses to the nucleocapsid protein (NP) and the N-terminal domain (NTD) of the spike protein. Although NTD directed antibodies are capable of neutralization, they only compensated the loss of RBD-NAbs to ancestral SARS-CoV-2 virus but not to the Omicron variant due to a substantial conformational change of Omicron NTD. This longitudinal clinical study monitored the immune response of the same cohort for every doses, shaping a relationship between the trajectory of immune focus and the dynamics of the neutralizing potency against the evolving virus. Our data reveal that immune responses could not be endlessly elevated, while suppression of heightened immune responses focusing on one subunit together with a shift of immune responses to other subunits would occur after repeated vaccination. Thus, an updated vaccine with more diverse epitopes capable of inducing NAbs against VOCs would be a future direction for boosters.
Generation of human nociceptor-enriched sensory neurons for the study of pain-related dysfunctions
Authors: Holzer Anna-Katharina , Karreman Christiaan , Suciu Ilinca , Furmanowsky Lara-Seline , Wohlfarth Harald , Loser Dominik , Dirks Wilhelm G , González Emilio Pardo , Leist Marcel
Published: February 2022

In vitro models of the peripheral nervous system would benefit from further refinements to better support studies on neuropathies. In particular, the assessment of pain-related signals is still difficult in human cell cultures. Here, we harnessed induced pluripotent stem cells (iPSCs) to generate peripheral sensory neurons enriched in nociceptors. The objective was to generate a culture system with signaling endpoints suitable for pharmacological and toxicological studies. Neurons generated by conventional differentiation protocols expressed moderate levels of P2X3 purinergic receptors and only low levels of TRPV1 capsaicin receptors, when maturation time was kept to the upper practically-useful limit of 6 weeks. As alternative approach, we generated cells with an inducible NGN1 transgene. Ectopic expression of this transcription factor during a defined time window of differentiation resulted in highly-enriched nociceptor cultures, as determined by functional (P2X3 and TRPV1 receptors) and immunocytochemical phenotyping, complemented by extensive transcriptome profiling. Single cell recordings of Ca2+-indicator fluorescence from >9,000 cells were used to establish the “fraction of reactive cells” in a stimulated population as experimental endpoint, that appeared robust, transparent and quantifiable. To provide an example of application to biomedical studies, functional consequences of prolonged exposure to the chemotherapeutic drug oxaliplatin were examined at non-cytotoxic concentrations. We found (i) neuronal (allodynia-like) hypersensitivity to otherwise non-activating mechanical stimulation that could be blocked by modulators of voltage-gated sodium channels; (ii) hyper-responsiveness to TRPV1 receptor stimulation. These findings and several other measured functional alterations indicate that the model is suitable for pharmacological and toxicological studies related to peripheral neuropathies.
Statistical Curve Models For Inferring 3D Chromatin Architecture
Authors: Tuzhilina Elena , Hastie Trevor , Segal Mark
Published: February 2022

Reconstructing three dimensional (3D) chromatin structure from conformation capture assays (such as Hi-C) is a critical task in computational biology, since chromatin spatial architecture plays a vital role in numerous cellular processes and direct imaging is challenging. We previously introduced Poisson metric scaling (PoisMS), a technique that models chromatin by a smooth curve, which yielded promising results. In this paper, we advance several ways for improving PoisMS. In particular, we address initialization issues by using a smoothing spline basis. The resulting SPoisMS method produces a sequence of reconstructions re-using previous solutions as warm starts. Importantly, this approach permits smoothing degree to be determined via cross-validation which was problematic using our prior B-spline basis. In addition, motivated by the sparsity of Hi-C contact data, especially when obtained from single-cell assays, we appreciably extend the class of distributions used to model contact counts. We build a general distribution-based metric scaling (DBMS) framework, from which we develop zero-inflated and Hurdle Poisson models as well as negative binomial applications. Illustrative applications make recourse to bulk Hi-C data from IMR90 cells and single-cell Hi-C data from mouse embryonic stem cells.
Inverted genomic regions between reference genome builds in humans impact imputation accuracy and decrease the power of association testing
Authors: Sheng Xin , Xia Lucy , Conti David V. , Haiman Christopher A. , Kachuri Linda , Chiang Charleston W. K.
Published: February 2022

Over the last two decades, the human reference genome has undergone multiple updates as we complete a linear representation of our genome. There are two versions of human references currently used in the biomedical literature, GRCh37/hg19 and GRCh38, and conversions between these versions are critical for quality control, imputation, and association analysis. In the present study we show that genomic coordinates for single nucleotide variants (SNVs) in regions inverted between different builds of the reference genome are erroneously converted by the TOPMed imputation server. Depending on the array type, we estimate the inappropriate conversions of variant coordinates would occur in about 2-5 Mb of the genome. Independent of the imputation server, however, in-house conversions of variant coordinates are routine yet impact of mapped variants to these inverted regions and its downstream analytical consequences are underrecognized. We observed that errors for palindromic variants in these inverted regions cannot be detected by standard quality control procedures and destabilize the local haplotype structure, leading to loss of imputation accuracy and power in association analyses. Though only a small proportion of the genome is affected, we show that these regions include important disease susceptibility variants that would be lost due to poor imputation. For example, we show that a known locus associated with prostate cancer on chr10 would have its association P-value drop from 2.86×10-7 to 0.0011 in a case-control analysis of 20,286 Africans and African Americans (10,643 cases and 9,643 controls). We devise a straight-forward heuristic based on the popular tool liftOver that can easily detect and correct these variants in the inverted regions between genome builds to locally improve imputation accuracy.
A pipeline for natural small molecule inhibitors of endoplasmic reticulum stress
Authors: da Silva Daniela Correia , Valentão Patrícia , Andrade Paula B. , Pereira David M.
Published: February 2022

The homeostasis of eukaryotic cells is inseverable of that of the endoplasmic reticulum (ER). The main function of this organelle is the synthesis and folding of a significant portion of cellular proteins, while also being the major calcium reservoir of the cell. Upon unresolved ER stress, a set of stress response signaling pathways that are collectively labeled as the unfolded protein response (UPR) is activated. Prolonged or intense activation of this molecular machinery may be deleterious. It is known that compromised ER homeostasis, and consequent UPR activation, characterize the pathogenesis of neurodegenerative disease.

In an effort to discover new small molecules capable of countering ER stress, we subjected a panel of over 100 natural molecules to a battery of assays designed to evaluate several hallmarks of ER stress. The effect of the compounds on calcium homeostasis, key gene and protein expression, and levels of protein aggregation were evaluated in fibroblasts, and subsequently in neuronal cells. This framework resulted in the identification of several bioactive molecules capable of countering ER stress and deleterious events associated to it, among which delphinidin stands out as the most promising candidate against neurodegeneration.
The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity
Authors: Petit Guillaume A. , Hong Yaoqin , Djoko Karrera Y. , Whitten Andrew E. , Furlong Emily J. , McCoy Airlie J. , Gulbis Jacqueline M. , Totsika Makrina , Martin Jennifer L. , Halili Maria A.
Published: February 2022

The introduction of disulfide bonds into periplasmic proteins is a critical process in many Gram-negative bacteria. The formation and regulation of protein disulfide bonds have been linked to the production of virulence factors. Understanding the different pathways involved in this process is important in the development of strategies to disarm pathogenic bacteria. The well characterized disulfide bond-forming (DSB) proteins play a key role by introducing or isomerizing disulfide bonds between cysteines in substrate proteins. Curiously, the suppressor of copper sensitivity C proteins (ScsCs), which are part of the bacterial copper-resistance response, share structural and functional similarities with DSB oxidase and isomerase proteins, including the presence of a catalytic thioredoxin domain. However, the oxidoreductase activity of ScsC varies with its oligomerization state, which depends on a poorly conserved N-terminal domain. Here, the structure and function of Caulobacter crescentus ScsC (CcScsC) have been characterized. It is shown that CcScsC binds copper in the copper(I) form with subpicomolar affinity and that its isomerase activity is comparable to that of Escherichia coli DsbC, the prototypical dimeric bacterial isomerase. It is also reported that CcScsC functionally complements trimeric Proteus mirabilis ScsC (PmScsC) in vivo, enabling the swarming of P. mirabilis in the presence of copper. Using mass photometry and small-angle X-ray scattering (SAXS) the protein is demonstrated to be trimeric in solution, like PmScsC, and not dimeric like EcDsbC. The crystal structure of CcScsC was also determined at a resolution of 2.6 Å, confirming the trimeric state and indicating that the trimerization results from interactions between the N-terminal α-helical domains of three CcScsC protomers. The SAXS data analysis suggested that the protomers are dynamic, like those of PmScsC, and are able to sample different conformations in solution.
Interactions between 2′-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors
Authors: Bueno Renata V. , Davis Samuel , Dawson Alice , Ondachi Pauline W. , Carroll F. Ivy , Hunter William N.
Published: February 2022

Low-nanomolar binding constants were recorded for a series of six 2′-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues with acetylcholine-binding protein (AChBP). The crystal structures of three complexes with AChBP reveal details of molecular recognition in the orthosteric binding site and imply how the other three ligands bind. Comparisons exploiting AChBP as a surrogate for α4β2 and α7 nicotinic acetylcholine receptors (nAChRs) suggest that the key interactions are conserved. The ligands interact with the same residues as the archetypal nAChR agonist nicotine yet display greater affinity, thereby rationalizing their in vivo activity as potent antagonists of nicotine-induced antinociception. An oxyanion-binding site is formed on the periphery of the AChBP orthosteric site by Lys42, Asp94, Glu170 and Glu210. These residues are highly conserved in the human α4, β2 and α7 nAChR sequences. However, specific sequence differences are discussed that could contribute to nAChR subtype selectivity and in addition may represent a point of allosteric modulation. The ability to engage with this peripheral site may explain, in part, the function of a subset of ligands to act as agonists of α7 nAChR.