bluuebunny/crossref_metadata_2025 huggingface dataset:
Delayed autumnal leaf senescence following nutrient fertilization results in altered nitrogen resorption
Authors: Wang Peilin , Fu Chen , Wang Liying , Yan Tao
Published: March 2022

Increased atmospheric nitrogen (N) deposition could create an imbalance between N and phosphorus (P), which may substantially impact ecosystem functioning. Changes in autumnal phenology (i.e., leaf senescence) and associated leaf nutrient resorption may profoundly impact plant fitness and productivity. However, we know little about how and to what extent nutrient addition affects leaf senescence in tree species, or how changes in senescence may influence resorption. We thus investigated the impacts of N and P addition on leaf senescence and leaf N resorption in 2-year-old larch (Larix principisrupprechtii) seedlings in northern China. Results showed that nutrient addition (i.e., N, P or N + P addition) significantly delayed autumnal leaf senescence, and decreased leaf N resorption efficiency (NRE) and proficiency (NRP), particularly in the N and N + P treatments. Improved leaf N concentrations were correlated with delayed leaf senescence, as indicated by the positive relationship between mature leaf N concentrations and the timing of leaf senescence. Following nutrient addition, larch seedlings shifted toward delayed onset, but more rapid, leaf senescence. Additionally, we observed an initial negative correlation between the timing of leaf senescence and NRE and NRP, followed by a positive correlation, indicating delayed and less efficient remobilization during the early stages of senescence, followed by accelerated resorption in the later stages. However, the latter effect was potentially impaired by the increased risk of early autumn frost damage, thus failed to fully compensate for the negative effects observed during the early stages of senescence. Improved soil P availability increased leaf N resorption and thus weakened the negative impact of delayed leaf senescence on leaf N resorption, so P addition had no significant impact on leaf N resorption. Overall, our findings clarify the relationship between nutrient addition–resorption and the linkage with leaf senescence, and would have important implications for plant nutrient conservation strategy and nutrient cycling.
Aridity and cold temperatures drive divergent adjustments of European beech xylem anatomy, hydraulics and leaf physiological traits
Authors: Vicente Eduardo , Didion-Gency Margaux , Morcillo Luna , Morin Xavier , Vilagrosa Alberto , Grossiord Charlotte
Published: March 2022

Understanding plant trait coordination and variance across climatic gradients is critical for assessing forests’ adaptive potential to climate change. We measured 11 hydraulic, anatomical and leaf-level physiological traits in European beech (Fagus sylvatica L.) along a moisture and temperature gradient in the French Alps. We assessed how traits covaried, and how their population-level variances shifted along the gradient. The intrapopulation variances of vessel size and xylem-specific conductivity reduced in colder locations as narrow vessels were observed in response to low temperature. This decreased individual-level water transport capacity compared with the warmer and more xeric sites. Conversely, the maximum stomatal conductance and Huber value variances were constrained in the arid and warm locations, where trees showed restricted gas exchange and higher xylem-specific conductivity. The populations growing under drier and warmer conditions presented wide variance for the xylem anatomical and hydraulic traits. Our results suggest that short-term physiological acclimation to raising aridity and heat in southern beech populations may occur mainly at the leaf level. Furthermore, the wide variance of the xylem anatomical and hydraulic traits at these sites may be advantageous since more heterogeneous hydraulic conductivity could imply populations’ greater tree–tree complementarity and resilience against climatic variability. Our study highlights that both intrapopulation trait variance and trait network analysis are key approaches for understanding species adaptation and the acclimation potential to a shifting environment.
XenostrobusorVignadula(Bivalvia: Mytilidae)? A taxonomic re-evaluation of small black mussels inhabiting the upper intertidal zone of the estuaries of Southeast Asia
Authors: Tan Koh Siang , Tan Samuel Hui Ming , Sanpanich Kitithorn , Duangdee Teerapong , Ambarwati Reni
Published: March 2022

The presence of small black mussels in the upper intertidal zone of estuarine seashores in Southeast Asia is often overlooked, despite their numerical dominance. Here, we clarify their species identities, taxonomy, geographical distributions and genetic relationships. Our molecular results suggest that three closely related species in East and Southeast Asia form a sister clade to Australian and New Zealand Xenostrobus. Given their distinctness, we resurrect the genus Vignadula to distinguish these two clades. Vignadula atrata, first described from Japan and type species of the genus, is confined to north-east Asia, whilst two other Vignadula species occur natively in Southeast Asia. Of these two species, one is found throughout Thailand, Malaysia, Singapore and Java. We show that this species corresponds to Xenostrobus balani and Xenostrobus mangle described from the Malacca Strait, which are genetically indistinguishable and here considered as one and the same species, Vignadula mangle comb. nov. The other species, Vignadula kuraburiensis sp. nov., described in this study, has so far been found only in south-west Thailand. Members of Vignadula are, in turn, all clearly different from their closest morphological equivalent in Australia, Xenostrobus pulex. A new subfamily Xenostrobinae is proposed to accommodate the two genera Xenostrobus and Vignadula.
Cow's milk allergy
Authors: Arasi Stefania , Cafarotti Arianna , Fiocchi Alessandro
Published: March 2022

Purpose of review

To highlight the most recent insights on cow's milk allergy (CMA), its treatment, and management.

Recent findings

CMA is one of the most common food allergies among children. Burdened by the risk for fatal reaction, CMA may imply also a severe impairment of health-related quality of life at individual and family level as well as well as individual and societal costs. The updated Diagnosis and Rationale for Action against Cow's Milk Allergy series is going to provide a series of manuscripts that will offer a comprehensive state-of-the-art specifically on CMA, including international evidence-based recommendations. The current results from randomized clinical trials highlight that oral immunotherapy may be effective by itself in providing desensitization. Preliminary data suggest that biologicals such as omalizumab may be able to increase the threshold of reactivity to milk or several foods (if multiple food allergies) without requiring allergen exposure. Breastfeeding is the first choice for infants with CMA. Extensively hydrolyzed formula and amino-acid formula are valid alternatives and may be particularly helpful when eliminating multiple foods, with severe complex gastrointestinal food allergies, eosinophilic esophagitis, severe eczema, or symptoms while exclusively breastfeeding. Heed is needed to ensure the formula is nutritionally sufficient. Due to a high degree of cross-reactivity with cow's milk proteins and risk for allergic reactions, goats’ milk or other mammals’ milk should not be used.

The adoption and implementation of evidence-based recommendations may guide a proper diagnostics and management and awaited advances in knowledge will allow the development of a personalized treatment tailored on the specific CMA patient's profile.
Association of Obesity With Longer Time to Pregnancy
Authors: Burger Taylor , Li Joanna , Zhao Qiuhong , Schreiber Courtney A. , Teal Stephanie , Turok David K. , Natavio Melissa , Peipert Jeffrey F.
Published: March 2022

OBJECTIVE:

To assess whether obesity is associated with increased time to pregnancy in a cohort of participants who were stopping their contraceptive method to attempt pregnancy.

METHODS:

We performed a secondary analysis of the FACT (Fertility After Contraceptive Termination) study. This prospective analysis included 432 participants, aged 18–35 years, who discontinued contraception to become pregnant, were sexually active with a male partner, and provided pregnancy status data within the first 12 months in the study. The primary outcome, time to pregnancy, was measured beginning with discontinuation of contraception to estimated pregnancy date. We used Cox proportional hazard models to assess associations of normal (lower than 25.0), overweight (25.0–29.9), and obese (30 or higher) body mass index (BMI) and time to pregnancy while controlling for potential confounding factors.

RESULTS:

After adjusting for confounders, participants with BMIs 30 or higher were noted to have prolonged time to pregnancy compared with those with BMIs lower than 25 (adjusted hazard ratio [aHR] 0.62; 95% CI 0.44–0.89). The median time to pregnancy for participants with normal BMIs was 5.3 months (95% CI 3.8–6.4) compared with 8.2 months (95% CI 6.8–10.8) for participants with obesity. Pregnancy rates at 1 year were 76.4% (95% CI 69.7–82.6%), 69.5% (95% CI 60.5–78.1%), and 59.1% (95% CI 51.0–67.4%) for participants with BMIs lower than 25, 25–29.9, and 30 or higher, respectively. Menstrual irregularity was also associated with decreased fertility (aHR 0.67; 95% CI 0.46–0.97).

CONCLUSION:

Compared with participants with normal BMIs, we observed increased time to pregnancy for participants with obesity stopping contraception with the intention to become pregnant. Understanding the reasons for this association will be helpful to inform patients and guide clinical practice.

FUNDING SOURCE:

The FACT Study was funded, in part, by Bayer, CooperSurgical, and the Society of Family Planning.
Exposure to Tramadol During Early Pregnancy and Risk of Spontaneous Abortion or Major Congenital Malformations
Authors: Sørensen Anne Mette Skov , Noergaard Mia Muusfeldt , Gotfredsen Ditte Resendal , Kjærbye-Thygesen Anette , Jimenez-Solem Espen , Askaa Bjarke , Poulsen Henrik Enghusen , Horwitz Henrik , Andersen Jon Trærup
Published: March 2022

OBJECTIVE:

To investigate whether exposure to tramadol during early pregnancy is associated with an increased risk of spontaneous abortion or major congenital malformations.

METHODS:

The study is a nationwide cohort study including all registered pregnancies in Denmark between January 1, 1997, and December 31, 2016. The Danish National Prescription Register was used to identify maternal exposure to tramadol. Pregnancies with maternal exposure to tramadol were matched with pregnancies without maternal exposure to tramadol in a ratio of up to 1:4 using propensity scoring. The primary outcomes were spontaneous abortion and major congenital malformations. Cox proportional hazards regression was used to estimate the hazard ratios (HRs) of spontaneous abortion, and log binominal models were used to estimate the relative risk ratios (RRs) of major congenital malformations.

RESULTS:

A total of 36,467 (tramadol exposure n=7,310) and 18,907 (tramadol exposure n=3,796) pregnancies were included in the analyses of spontaneous abortion and major congenital malformations, respectively. Spontaneous abortion occurred in 893 (12.2%) pregnancies with maternal exposure to tramadol and in 3,471 (11.9%) pregnancies without maternal exposure to tramadol (HR 1.06, 95% CI 0.99–1.14). A major congenital malformation occurred in the offspring of 151 (4.0%) pregnancies with maternal exposure to tramadol, compared with 579 (3.8%) in pregnancies without maternal exposure to tramadol (RR 1.04, 95% CI 0.87–1.24).

CONCLUSION:

Exposure to tramadol during early pregnancy does not appear to be associated with an increased risk of spontaneous abortion or major congenital malformations.
Accidental Flibanserin Ingestion in Children Causing Acute Respiratory and Central Nervous System Depression
Authors: Whitaker Marcea B. , Chehab Miriam M. , Chang Christina Y. , McCulley Lynda V. , Sewell Catherine A.
Published: March 2022

This commentary serves to raise awareness for health care professionals about the potential risks of accidental ingestion of flibanserin tablets by children. Flibanserin was approved by the U.S. Food and Drug Administration (FDA) for the treatment of acquired generalized hypoactive sexual desire disorder in premenopausal women. Since its approval in 2015, the FDA has identified five reports of serious accidental ingestion by toddlers. All five children, boys with ages ranging from 18 months to 2 years, presented with central nervous system and respiratory depression, and two of them required intubation. A combination of hypertension, hyperthermia, and seizure-like activity was also seen in four of the five children. The clinical manifestation resembles serotonin syndrome (eg, tachycardia, hypertension, and muscle stiffness). As flibanserin use increases, greater awareness by health care professionals regarding the risk of accidental pediatric ingestion is needed to facilitate preventative counseling for patients with young children.
Virtual orthopaedic surgery away rotation benefits both the program and applicant: a survey of participants
Authors: White Micah , Montgomery Corey , Romer Karen , Kelly Derek M.
Published: March 2022

Background:

The COVID-19 pandemic has forced many medical education institutions to switch from in-person to online learning environments. There is an existing gap in knowledge about the effectiveness of virtual learning for medical students.

Objective:

The purpose of the study was to determine if virtual orthopaedic surgery away rotations (VOSAR) benefit medical students and programs.

Methods:

Virtual rotations were created at two large residency programs for fourth-year medical students. From October 12, 2020 through December 28, 2020, satisfaction and quality were assessed using a 22-question survey, residency interview, rank, and match data. Forty-two fourth-year medical students participated, 38 of whom responded to the survey.

Results:

Most students stated course objectives were clear and consistent with coursework. Most were pleased with the variety of cases and presentations and were able to meaningfully interact with faculty and residents. Most stated they would participate again and suggest the rotation to others. Twenty-five of 42 participants were ranked by at least one program; 39 were accepted into residency positions, 21 of which were in orthopaedic surgery.

Conclusions:

The results indicate that the VOSAR benefits students and programs. Based on the success of the VOSAR, both programs continued to offer the curriculum for 2021.

Level of Evidence:

Level IV.
Osgood-Schlatter disease: a review of current diagnosis and management
Authors: Ciatawi Kartini , Dusak I. Wayan Suryanto
Published: March 2022

Osgood-Schlatter disease is a common cause of knee pain in children and adolescents, particularly in those who participate in sports. Repetitive force during athletic activities, along with changes that happen during a growth spurt, result in the development of traction apophysitis. Because of its typical presentation, the diagnosis is usually made clinically. The disorder generally resolves with skeletal maturity, and most patients respond to conservative therapy. Surgery can be considered in recalcitrant cases. Several approaches of surgical intervention have been proposed; each approach has its advantages and disadvantages.
Team-based strategies to prevent heart failure
Authors: Taha Mohamad B. , Patel Kershaw V. , Nasir Khurram
Published: March 2022

Purpose of review

The burden of heart failure (HF) in the United States and worldwide is projected to rise. Prevention of HF can curb the burden of this chronic syndrome, but current approaches are limited. This review discusses team-based strategies aimed to prevent HF.

Recent findings

Individuals at high risk for developing HF can be identified using HF risk scores, biomarkers, and cardiac imaging. Electronic medical records (EMR) can integrate clinical data to estimate HF risk and identify individuals who may benefit most from preventive therapies. Team-based interventions can lead to enhanced adherence to medications, optimization of medical management, and control of risk factors. Multifaceted interventions involve EMR-based strategies, pharmacist- and nurse-led initiatives, involvement of community personnel, polypills, and digital solutions.

Team-based strategies aimed to prevent HF incorporate a broad group of personnel and tools. Despite implementation challenges, existing resources can be efficiently utilized to facilitate team-based approaches to potentially reduce the burden of HF.
Psychiatric Symptoms Across the Menstrual Cycle in Adult Women: A Comprehensive Review
Authors: Handy Ariel B. , Greenfield Shelly F. , Yonkers Kimberly A. , Payne Laura A.
Published: March 2022

Learning objective

After participating in this activity, learners should be better able to:

• Discuss and outline the general and overlapping effects of the menstrual cycle on women’s mental health

A growing body of research demonstrates menstrual cycle–dependent fluctuations in psychiatric symptoms; these fluctuations can therefore be considered as prevalent phenomena. Possible mechanisms underlying these fluctuations posit behavioral, psychological, and neuroendocrine influences. Recent reviews document cyclic exacerbation of symptoms and explore these mechanisms in the context of specific and often single disorders. The question remains, however, as to whether there are general and overlapping effects of the menstrual cycle on women’s mental health. To address this gap, we synthesized the literature examining the exacerbation of a variety of psychiatric symptoms across the menstrual cycle in adult women. Results show that the premenstrual and menstrual phases are most consistently implicated in transdiagnostic symptom exacerbation. Specifically, strong evidence indicates increases in psychosis, mania, depression, suicide/suicide attempts, and alcohol use during these phases. Anxiety, stress, and binge eating appear to be elevated more generally throughout the luteal phase. The subjective effects of smoking and cocaine use are reduced during the luteal phase, but fewer data are available for other substances. Less consistent patterns are demonstrated for panic disorder, symptoms of posttraumatic stress disorder, and borderline personality disorder, and it is difficult to draw conclusions for symptoms of generalized anxiety disorder, social anxiety disorder, obsessive-compulsive disorder, and trichotillomania because of the limited data. Future research should focus on developing standardized approaches to identifying menstrual cycle phases and adapting pharmacological and behavioral interventions for managing fluctuations in psychiatric symptoms across the menstrual cycle.
Brolucizumab for the treatment of diabetic macular edema
Authors: Kuo Blanche L. , Singh Rishi P.
Published: March 2022

Purpose of review

To review the available data supporting the use of brolucizumab in the treatment of diabetic macular edema (DME).

Recent findings

Brolucizumab is a humanized single- chain variable antibody fragment (scFv), the smallest functional subunit of an antibody approved for intravitreal use. Three phase III studies demonstrate that at 52 weeks, brolucizumab has statistically superior anatomical outcomes of reducing retinal thickness (54.0–57.5% of brolucizumab treated eyes achieved central subfield thickness <280 μm compared to 40.1 – 41.4% of aflibercept treated eyes) and retinal fluid (present in 54.2–60.3% of brolucizumab treated eyes compared to 72.9–78.2% of aflibercept treated eyes). Brolucizumab also demonstrated a prolonged durability up to 16 weeks, thus reducing treatment burden. The visual outcomes appear noninferior to current anti-VEGF agents with an increased risk for intraocular inflammatory events (0.3–4.7% compared to 0.6–1.7%).

Results from recent phase III trials showing the efficacy and safety of brolucizumab presents an additional therapeutic option in the DME treatment landscape. It can reduce treatment burden in DME with increased inter-treatment intervals while conferring efficacy in both functional and anatomical outcomes. Caution should be taken regarding the risks of intraocular inflammation, retinal vasculitis, and retinal vascular occlusion.
Intramuscular Stem Cell Injection in Combination with Bioengineered Nerve Repair or Nerve Grafting Reduces Muscle Atrophy
Authors: Schaakxs Dominique , Wiberg Mikael , Kingham Paul J. , Kalbermatten Daniel F.
Published: March 2022

Background:

Peripheral nerve injuries represent a clinical challenge, especially when they are accompanied by loss of neural tissue. In this study, the authors attempted to attain a better outcome after a peripheral nerve injury by both repairing the nerve lesion and treating the denervated muscle at the same time.

Methods:

Rat sciatic nerves were transected to create 10-mm gaps. Repair was performed in five groups (n = 5 rats for each), as follows: group 1, nerve repair using poly-3-hydroxybutyrate strips to connect the proximal and distal stumps, in combination with control growth medium injection in the gastrocnemius muscle; group 2, nerve repair with poly-3-hydroxybutyrate strip seeded with Schwann cell-like differentiated adipose stem cells (differentiated adipose stem cell strip) in combination with growth medium intramuscular injection; group 3, differentiated adipose stem cell strip in combination with intramuscular injection of differentiated adipose stem cells; group 4, repair using autograft (reverse sciatic nerve graft) in combination with intramuscular injection of growth medium; and group 5, autograft in combination with intramuscular injection of differentiated adipose stem cells. Six weeks after nerve injury, the effects of the stem cells on muscle atrophy were assessed.

Results:

Poly-3-hydroxybutyrate strips seeded with differentiated adipose stem cells showed a high number of βIII-tubulin–positive axons entering the distal stump and abundant endothelial cells. Group 1 animals exhibited more muscle atrophy than all the other groups, and group 5 animals had the greatest muscle weights and muscle fibers size.

Conclusion:

Bioengineering nerve repair in combination with intramuscular stem cell injection is a promising technique to treat nerve lesions and associated muscle atrophy.

Clinical Relevance Statement:

Nerve injuries and resulting muscle atrophy are a clinical challenge. To optimize functional recovery after a nerve lesion, the authors treated the nerve and muscle at the same time by using regenerative medicine with adipose stem cells and obtained encouraging results for future clinical applications.
Procurement of Deceased Donor Parathyroid Glands With the Aid of Near-infrared Autofluorescence Imaging
Authors: Ward Casey J. , Kelly Yvonne M. , Syed Shareef M. , Meier Raphael P.H. , Ando Tadasuke , Wisel Steven A. , Gardner James M. , Stock Peter G. , Duh Quan-Yang
Published: March 2022

Background.

Parathyroid allotransplantation is a burgeoning treatment for severe hypoparathyroidism. Deceased donor parathyroid gland (PTG) procurement can be technically challenging due to lack of normal intraoperative landmarks and exposure constraints in the neck of organ donors. In this study, we assessed standard 4-gland exposure in situ and en bloc surgical techniques for PTG procurement and ex vivo near-infrared autofluorescence (NIRAF) imaging for identification of PTGs during organ recovery.

Methods.

Research tissue consent was obtained from organ donors or donor families for PTG procurement. All donors were normocalcemic, brain-dead, solid organ donors between 18 and 65 y of age. PTGs were procured initially using a standard 4-gland exposure technique in situ and subsequently using a novel en bloc resection technique after systemic organ preservation flushing. Parathyroid tissue was stored at 4 °C in the University of Wisconsin solution up to 48 h post-procurement. Fluoptics Fluobeam NIRAF camera and Image J software were utilized for quantification of NIRAF signal.

Results.

Thirty-one brain-dead deceased donor PTG procurements were performed by abdominal transplant surgeons. In the initial 8 deceased donors, a mean of 1.75 glands (±1.48 glands SD) per donor were recovered using the 4-gland in situ technique. Implementation of combined en bloc resection with ex vivo NIRAF imaging in 23 consecutive donors yielded a mean of 3.60 glands (±0.4 SD) recovered per donor (P < 0.0001). Quantification of NIRAF integrated density signal demonstrated >1-fold log difference in PTG (2.13 × 105 pixels) versus surrounding anterior neck structures (1.9 × 104 pixels; P < 0.0001). PTGs maintain distinct NIRAF signal from the time of recovery (1.88 × 105 pixels) up to 48 h post-procurement (1.55 × 105 pixels) in organ preservation cold storage (P = 0.34).

Conclusions.

The use of an en bloc surgical technique with ex vivo NIRAF imaging significantly enhances the identification and recovery of PTG from deceased donors.
Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR
Authors: Hinkel Lauren A. , Willsey Graham G. , Lenahan Sean M. , Eckstrom Korin , Schutz Kristin C. , Wargo Matthew J.
Published: March 2022

Glutamine amidotransferase-1 domain-containing AraC-family transcriptional regulators (GATRs) are present in the genomes of many bacteria, including all

Pseudomonas

species. The involvement of several characterized GATRs in amine-containing compound metabolism has been determined, but the full scope of GATR ligands and regulatory networks are still unknown. Here, we characterize

Pseudomonas putida

’s detection of the animal-derived amine compound creatine, a compound particularly enriched in muscle and ciliated cells by a creatine-specific GATR, PP_3665, here named CahR (Creatine amidohydrolase Regulator). cahR is necessary for transcription of the gene encoding creatinase (PP_3667/creA) in the presence of creatine and is critical for P. putida’s ability to utilize creatine as a sole source of nitrogen. The CahR/creatine regulon is small, and an electrophoretic mobility shift assay demonstrates strong and specific CahR binding only at the creA promoter, supporting the conclusion that much of the regulon is dependent on downstream metabolites. Phylogenetic analysis of creA orthologues associated with cahR orthologues highlights a strain distribution and organization supporting probable horizontal gene transfer, particularly evident within the genus

Acinetobacter

. This study identifies and characterizes the GATR that transcriptionally controls

P. putida

’s metabolism of creatine, broadening the scope of known GATR ligands and suggesting GATR diversification during evolution of metabolism for aliphatic nitrogen compounds.
Effect of a Pilates exercise program on the flexion-relaxation rate in women with chronic low back pain
Authors: Ferri-Caruana Ana , Romagnoli Marco , Salazar-Bonet Lluis Raimon , Staiano Walter
Published: March 2022

Purpose

To evaluate the effect of a Pilates exercise program (PEP) on FRR and FRR asymmetry of the erector spinae (ES) muscle during standing maximal trunk flexion/extension in women with chronic low-back pain (LBP). A secondary goal was to investigate the effect of PEP on full trunk flexion ROM (TFRoM), pain intensity and functional capacity and analyse their relationship with the FRR.

Material and methods

Thirty women with chronic LPB were randomly assigned to either PEP (EG, n=15) or control group (CG=15). EG followed an 8-week PEP while no specific intervention was carried out on the controls. Before and after this period all variables were recorded.

Results

FRR did not show any significant changes between or within groups (p>0.05). EG showed a significant statistical difference in the FRR asymmetry pre- and post-intervention (p□ 0.05). Full TFRoM did not show any significant changes between or within groups (p>0.05). EG showed a significant decrease of 30% on pain intensity and a significant increase of 13.4 % in functional capacity (P□0.001) from pre to post-intervention.

Conclusions

An 8-week PEP does not affect FRR nor full trunk ROM, however yields improvements in pain intensity and functional capacity.Professionals should be aware of the negative effect on FRR asymmetry.
Predicting pneumothorax after lung biopsy from pre-operative imaging using a deep convolutional neural network
Authors: Jang Seong Jun , Pua Bradley B. , Shih George
Published: March 2022

Background

Pneumothorax remains one of the most common complications after computed tomography (CT)–guided lung biopsies. Radiographic features including bullae and nodule size are possible markers for post-biopsy pneumothorax. We determine whether a convolutional neural network (CNN) can accurately predict a pneumothorax after lung biopsy based on pre-operative imaging alone.

Methods

With institutional review board approval, we retrospectively evaluated 3,822 patients who underwent a CT-guided lung biopsy between 2011 to 2019. Two image sets were created with CT scout images (1300 patients, 650 pneumothoraces) and chest x-rays (CXR) taken within three months pre-procedure (884 patients, 140 pneumothoraces). Using pre-operative images, CNNs of varying layer depths were trained using transfer learning to predict the development of a pneumothorax post-biopsy. Performance against models were compared using sensitivity analysis and the McNemar’s test.

Results

The CNN models trained with CT scout images performed near chance. However, the models performed better with CXR radiographs taken within three months pre-biopsy. For the anterior-posterior view, sensitivity was 0.40, specificity was 0.89, PPV was 0.43, and NPV was 0.87 (AUC = 0.67). For the lateral view, sensitivity was 0.40, specificity was 0.80, PPV was 0.32, and NPV was 0.86 (AUC = 0.65). Increasing CNN layers did not affect performance (p > 0.05).

Conclusion

Chest radiographs taken within three months of lung biopsy may provide important radiographic information for CNNs to assess pneumothorax risk in patients prior to CT-guided lung biopsies. However, more baseline and standardized CXRs before biopsies are necessary to create a robust model for clinical application.
The clinical need for clustered AChR cell-based assay testing of seronegative MG
Authors: Masi Gianvito , Li Yingkai , Karatz Tabitha , Pham Minh C. , Oxendine Seneca R. , Nowak Richard J. , Guptill Jeffrey T. , O’Connor Kevin C.
Published: March 2022

Trial eligibility in myasthenia gravis (MG) remains largely dependent on a positive autoantibody serostatus. This significantly hinders seronegative MG (SNMG) patients from receiving potentially beneficial new treatments. In a subset of SNMG patients, acetylcholine receptor (AChR) autoantibodies are detectable by a clustered AChR cell-based assay (CBA). Of 99 SNMG patients from two academic U.S. centers, 18 (18.2%) tested positive by this assay. Autoantibody positivity was further validated in 17/18 patients. In a complementary experiment, circulating AChR-specific B cells were identified in a CBA-positive SNMG patient. These findings corroborate the clinical need for clustered AChR CBA testing when evaluating SNMG patients.
Growth monitoring and promotion service utilization and associated factors among children under-two years of age in Samara–logia city of Afar Region, Northeast Ethiopia
Authors: Kiros Semhal , Mohammed Ibrahim , Ahmed Kedir Y.
Published: March 2022

Introduction

Utilizing growth monitoring and promotion (GMP) during the first two years of birth helps to detect common childhood health problems (e.g., malnutrition and infections) at early stages and offers an opportunity for promoting education and nutritional counselling. However, no previously published study has investigated the level of GMP utilization and associated factors among pastoralist Ethiopian mothers including the Afar National and Regional State (ANRS), where under-nutrition is the major cause of childhood morbidity and mortality. This is the first study aimed to investigate the utilization and associated factors of GMP service for infants and young children in the ANRS of Ethiopia.

Methods

A community-based cross-sectional study was conducted from May to June 202 in the Samara-logia city administration. A total of 416 children aged two years were selected using a random sampling technique, and an interviewer-administered questionnaire was used to collect data. Multivariable logistic regression was applied to examine the influence of explanatory variables (including socio-demographic, obstetric and health service, and health literacy factors) on the utilization of GMP services.

Results

The overall utilization of GMP for infants and children was 15.9% with 95% confidence intervals (CI) from 12.0% to 19.5%. Children whose fathers attained college or higher schooling were more likely to utilize GMP services (AOR = 12.40; 95% CI: 4.15, 37.4). Children who resided in households with a higher number of children were less likely to utilize GMP services (AOR = 0.10; 95%CI: 0.03, 0.26 for households with 3-4 children and AOR = 0.16; 95% CI: 0.05, 0.48 for children with 4+). The odds for GMP service utilization was significantly higher among children who received postnatal care (AOR = 9.68; 95% CI: 3.57, 26.20).

Conclusion

The utilization of GMP services is lower to support the reduction of child morbidity and mortality attributed to malnutrition for infants and children in Ethiopia. A higher level of schooling and those who received postnatal care were more likely to utilize GMP, while those who were from households with a higher number of children were less likely to utilize GMP. Our findings suggest strengthening GMP service in Ethiopia, and focused efforts are required on the modifiable associated factors.
A Genomic Snapshot of Enterococcus faecalis within Public Hospital Environments in South Africa
Authors: Shobo Christiana O. , Amoako Daniel G. , Allam Mushal , Ismail Arshad , Essack Sabiha Y. , Bester Linda A.
Published: March 2022

Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, genetic support, clones and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C and D) in Durban, South Africa. Following microbial identification and antibiotic susceptibility tests. Of the 245 E. faecalis isolates identified, 38 were subjected to WGS on the Illumina MiSeq platform. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic resistome found in isolates originating from the different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n=11) and prophages (n=14), that were mostly clone-specific. Of note, a large number insertion sequence (IS) families were found with the IS3 (55%), IS5 (42%), IS1595 (40%) and Tn3 Transposon been the most predominate. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n =7), ST40 (n = 6), ST21 (n =5), ST126 (n = 3), ST23 (n =3) and ST386 (n=3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intra-clonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into E. faecalis in the hospital environments relevant in the design of optimal infection prevention strategies in hospital settings.
Processing Stage Flexibility of the SNARC effect: Task Relevance or Magnitude Relevance?
Authors: Xiang Xinrui , Yan Lizhu , Fu Shimin , Nan Weizhi
Published: March 2022

Previous studies have shown that the processing stage of the spatial-numerical association of response codes (SNARC) effect was flexible. Two recent studies by Nan et al. (2021) and Yan et al. (2021) used the same experimental paradigm to check whether the SNARC effect occurred in the semantic-representation stage but reached contradictory conclusions, showing that the SNARC effect was influenced by a magnitude Stroop effect in a magnitude comparison task but not by a parity Stroop effect in a parity judgment task. The two studies had two distinct operational factors: the task type (magnitude comparison task or parity judgment task, with the numerical magnitude information task-relevant or task-irrelevant) and the semantic representation stage-related interference information (magnitude or parity Stroop effect, with the interference information magnitude-relevant or magnitude-irrelevant). To determine which factor influenced the SNARC effect, in the present study, the Stroop effect was switched in the two tasks based on the previous studies. The findings of four experiments consistently showed that the SNARC effect was not influenced by the parity Stroop effect in the magnitude comparison task but was influenced by the magnitude Stroop effect in the parity judgment task. Combined with the results of Nan et al. (2021) and Yan et al. (2021), the findings indicated that regardless of the task type or the task-relevance of numerical magnitude information, magnitude-relevant interference information was the primary factor to affect the SNARC effect. Furthermore, a two-stage processing model that explained the observed flexibility of the SNARC effect was proposed and discussed.

Public Significance Statement

Previous studies have shown that the spatial-numerical association of response codes (SNARC) effect is flexible in the direction and processing stage. The task type and interference information might be two influential factors for the flexibility of the SNARC effect. The present study reported that magnitude-relevant interference information, regardless of task type, was a crucial role to affect the SNARC effect. Moreover, a two-stage processing model was proposed to reveal the processing pathway of the SNARC effect and provided a possible explanation for the longstanding debate about the processing stage of the SNARC effect.
High-throughput analysis of dendritic and axonal arbors reveals transcriptomic correlates of neuroanatomy
Authors: Gliko Olga , Mallory Matt , Dalley Rachel , Gala Rohan , Gornet James , Zeng Hongkui , Sorensen Staci , Sumbul Uygar
Published: March 2022

Neuronal anatomy is central to the organization and function of brain cell types. However, anatomical variability within apparently homogeneous populations of cells can obscure such insights. Here, we report large-scale automation of neuronal morphology reconstruction and analysis on a dataset of 813 inhibitory neurons characterized using the Patch-seq method, which enables measurement of multiple properties from individual neurons, including local morphology and transcriptional signature. We demonstrate that these automated reconstructions can be used in the same manner as manual reconstructions to understand the relationship between some, but not all, cellular properties used to define cell types. We uncover gene expression correlates of laminar innervation on multiple transcriptomically defined neuronal subclasses and types. In particular, our results reveal correlates of the variability in Layer 1 (L1) axonal innervation in a transcriptomically defined subpopulation of Martinotti cells in the adult mouse neocortex.
The transcription factor network of E. coli steers global responses to shifts in RNAP concentration
Authors: Almeida Bilena L B , Bahrudeen Mohamed N M , Chauhan Vatsala , Dash Suchintak , Kandavalli Vinodh , Häkkinen Antti , Lloyd-Price Jason , Palma Cristina S D , Baptista Ines S C , Gupta Abhishekh , Kesseli Juha , Dufour Eric , Smolander Olli-Pekka , Nykter Matti , Auvinen Petri , Jacobs Howard T , Oliveira Samuel M D , Ribeiro Andre S
Published: March 2022

The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
Integrative analysis to identify shared mechanisms between schizophrenia and bipolar disorder and their comorbidities
Authors: Bharadhwaj Vinay Srinivas , Mubeen Sarah , Sargsyan Astghik , Jose Geena Mariya , Geissler Stefan , Hofmann-Apitius Martin , Domingo-Fernández Daniel , Kodamullil Alpha Tom
Published: March 2022

Schizophrenia and bipolar disorder are characterized by highly similar neuropsychological signatures, implying shared neurobiological mechanisms between these two disorders. These disorders also have comorbidities with other indications, such as type 2 diabetes mellitus (T2DM). To date, an understanding of the mechanisms that mediate the link between these two disorders remains incomplete. In this work, we identify and investigate shared patterns across multiple schizophrenia, bipolar disorder and T2DM gene expression datasets through multiple strategies. Firstly, we investigate dysregulation patterns at the gene-level and compare our findings against disease-specific knowledge graphs (KGs). Secondly, we analyze the concordance of co-expression patterns across datasets to identify disease-specific as well as common pathways. Thirdly, we examine enriched pathways across datasets and disorders to identify common biological mechanisms between them. Lastly, we investigate the correspondence of shared genetic variants between these two disorders and T2DM as well as the disease-specific KGs. In conclusion, our work reveals several shared candidate genes and pathways, particularly those related to the immune and nervous systems, which we propose mediate the link between schizophrenia and bipolar disorder and its shared comorbidity, T2DM.
Community structure determines the predictability of population collapse
Authors: Baruah Gaurav , Ozgul Arpat , Clements Christopher F.
Published: March 2022

Early warning signals (EWS) are phenomenological tools that have been proposed as predictors of the collapse of biological systems. Whilst a growing body of work has shown the utility of EWS based on either statistic derived from abundance data or shifts in phenotypic traits such as body size, so far this work has largely focused on single species populations.

However, in order to predict reliably the future state of ecological systems which inherently could consist of multiple species, understanding how reliable such signals are in a community context is critical.

Here, reconciling quantitative genetics and Lotka-Volterra equations which allow us to track both abundance and mean traits, we simulate the collapse of populations embedded in mutualistic and multi-trophic predator-prey communities. Using these simulations and warning signals derived from both population- and community-level data, we show that the utility of abundance-based EWS as well as metrics derived from stability-landscape theory (e.g., width and depth of the basin of attraction) are fundamentally linked, and thus the depth and width of the stability landscape could be used to identify which species should exhibit the strongest EWS of collapse.

The probability a species displays both trait and abundance based EWS is dependent on its position in a community, with some species able to act as indicators species. In addition, our results also demonstrate that in general trait-based EWS appear less reliable in comparison to abundance-based EWS in forecasting species collapses in our simulated communities. Furthermore, community-level abundance-based EWS were fairly reliable in comparison to their species-level counterparts in forecasting species level collapses.

Our study suggests a holistic framework that combines abundance-based EWS and metrics derived from stability-landscape theory that may help in forecasting species loss in a community context.
Distribution of Critical Areas for Ecological Conservation in Multiple Scenarios——Emphasizing the Impact of Human Activities
Authors: Dai Xinyan , Wang Hongwei , Ma Chen , Wang Xiaoqin , Zhou Jing , Tan Bo
Published: March 2022

Determining critical ecological protected areas at the city (county) spatial scale is crucial for coordinating regional ecological environment management, control, and governance. It is a recognized consensus in academia that human activities significantly impact natural ecosystems. Many scholars ignore this point in the research process and only use several factors to characterize human influence. Therefore, this study takes Aksu City and Wensu County, important cities and towns in southern Xinjiang, as examples, focusing on the impact of human activities on the distribution of critical ecological protection areas. First, we simulated the range, intensity, and local natural conditions of human activities in the study area using geospatial data. We created corresponding resistance surfaces (human activity resistance surface and natural landscape resistance surface). We then assign different weights to the two resistance surfaces based on several possible scenarios, resulting in different synthetic resistance surfaces. Finally, we used the Linkage Mapper plugin to identify critical ecological reserves and compared several results. The results show that: Human activities have greatly interfered with the migration and dispersal of species, affecting the distribution of critical ecological reserves. The specific performance is that in the urban center area with high intensity of human activities, the number and location of the surrounding ecological corridors change significantly with the increase in the proportion of human activity resistance and the total area remains unchanged; As part of the ecological corridors, the ecological pinch points changes with the location of the corridor, and the whole area remains unchanged; The threshold range of the restoration value of ecological barrier points is reduced. The maximum value generated by the restoration of ecological barrier points is reduced, which shows that the restoration value of ecological barrier points decreases with increased human activities.