bluuebunny/crossref_metadata_2025 huggingface dataset:
Rhomboid intercostal block or thoracic paravertebral block for postoperative recovery quality after video-assisted thoracic surgery
Authors: Wang Xuru , Jia Xiaoyu , Li Zhenping , Zhou Qinghe
Published: June 2023

BACKGROUND

The analgesic characteristics of rhomboid intercostal block (RIB) remain unclear. Before it can be fully recommended, we compared the recovery quality and analgesic effects of RIB and thoracic paravertebral block (TPVB) for video-assisted thoracoscopic surgery (VATS).

OBJECTIVE

The current study aimed to investigate whether there is a difference in postoperative recovery quality between TPVB and RIB.

DESIGN

A prospective, non-inferiority, randomised controlled trial.

SETTING

Affiliated Hospital of Jiaxing University in China from March 2021 to August 2022.

PATIENTS

Eighty patients aged 18 to 80 years, with ASA physical status I to III, and scheduled for elective VATS were enrolled in the trial.

INTERVENTION

Ultrasound-guided TPVB or RIB was performed with 20 ml 0.375% ropivacaine.

MAIN OUTCOME MEASURES

The primary outcome of the study was the mean difference of quality of recovery-40 scores 24 h postoperatively. The non-inferiority margin was defined as 6.3. Numeric rating scores (NRS) for pain at 0.5, 1, 3, 6, 12, 24 and 48 h postoperatively in all patients were also recorded.

RESULTS

A total of 75 participants completed the study. The mean difference of quality of recovery-40 scores 24 h postoperatively was −1.6 (95% CI, −4.5 to 1.3), demonstrating the non-inferiority of RIB to TPVB. There was no significant difference between the two groups in the area under the curve for pain NRS over time, at rest and on movement, at 6, 12, 24 and 48 h postoperatively (all P > 0.05), except for the area under the curve pain NRS over time on movement at 48 h postoperatively (P = 0.046). There were no statistical differences between the two groups in the postoperative sufentanil use at 0 to 24 h or 24 to 48 h (all P > 0.05).

CONCLUSION

Our study suggests that RIB was non-inferior to TPVB for the quality of recovery, with almost the same postoperative analgesic effect as TPVB after VATS.

CLINICAL TRIAL REGISTRATION

chictr.org.cn: ChiCTR2100043841.
Elevated FBXL18 promotes RPS15A ubiquitination and SMAD3 activation to drive HCC
Authors: Yu Hong-Qiang , Li Feng , Xiong HaoJun , Fang Lei , Zhang Jie , Bie Ping , Xie Chuan-Ming
Published: June 2023

Background:

F-box and leucine-rich repeat protein 18 (FBXL18) is an E3 ubiquitin ligase that is reported to be involved in the tumorigenesis of various types of cancer. However, it remains unknown whether FBXL18 is correlated with hepatocarcinogenesis.

Methods and results:

In the current study, we found that FBXL18 was highly expressed in HCC tissues and positively associated with poor overall survival of HCC patients. FBXL18 was an independent risk factor for HCC patients. We observed that FBXL18 drove HCC in FBXL18 transgenic mice. Mechanistically, FBXL18 promoted the K63-linked ubiquitination of small-subunit ribosomal protein S15A (RPS15A) and enhanced its stability, increasing SMAD family member 3 (SMAD3) levels and translocation to the nucleus and promoting HCC cell proliferation. Moreover, the knockdown of RPS15A or SMAD3 significantly suppressed FBXL18-mediated HCC proliferation. In clinical samples, elevated FBXL18 expression was positively associated with RPS15A expression.

Conclusion:

FBXL18 promotes RPS15A ubiquitination and upregulates SMAD3 expression, leading to hepatocellular carcinogenesis, and this study provides a novel therapeutic strategy for HCC treatment by targeting the FBXL18/RPS15A/SMAD3 pathway.
Comparison of implantation of posterior chamber phakic IOL implantation and laser vision correction in terms of corneal endothelial cells: 3-year observational paired-eye study
Authors: Choi Hannuy , Ryu Ik Hee , Lee In Sik , Kim Jin Kuk , Yoo Tae Keun
Published: June 2023

Purpose:

To compare the postoperative endothelial cell counts of EVO-implantable collamer lenses (ICLs) with a central hole (V4c and V5) and laser vision correction surgery (laser in situ keratomileusis or photorefractive keratectomy).

Setting:

B&VIIT Eye Center, Seoul, South Korea.

Design:

Retrospective observational and paired contralateral study.

Methods:

62 eyes of 31 patients who underwent EVO-ICLs with a central hole implantation in one eye (phakic intraocular lens [pIOL] group) and laser vision correction in the contralateral eye (LVC group) to correct refractive errors were retrospectively reviewed. Central endothelial cell density (ECD), percentage of hexagonal cells (HEX), coefficient of variation (CoV) in cell size, and adverse events were evaluated for at least 3 years. The endothelial cells were observed using a noncontact specular microscope.

Results:

All surgeries were performed, without complications during the follow-up period. The mean ECD loss values compared with the preoperative measurements were 6.65% and 4.95% during the 3 years after pIOL and LVC, respectively. There was no significant difference in ECD loss compared with the preoperative values (paired t test, P = .188) between the 2 groups. No significant loss in ECD was observed at any timepoint. The pIOL group showed higher HEX (P = .018) and lower CoV (P = .006) values than the LVC group at the last visit.

Conclusions:

According to the authors' experience, the EVO-ICL with a central hole implantation was a safe and stable vision correction method. Moreover, it did not induce statistically significant changes in ECD at 3 years postoperatively compared with LVC. However, further long-term follow-up studies are required to confirm these results.
Prevalence and Correlates of Cardiovascular, Pulmonary, Cancer, and Mental Health Comorbidities Among Adults With HIV Who Smoke
Authors: Elf Jessica L. , Horn Kimberly , Abroms Lorien , Stanton Cassandra A. , Cohn Amy M. , Spielberg Freya , Gray Tiffany , Harvey Emily , Debnam Charles , Kierstead Lexi , Levy Matthew E. , Castel Amanda , Monroe Anne , Niaura Raymond
Published: June 2023

Using data from the D.C. Cohort Longitudinal HIV Study, we examined (a) diagnosed mental health and (b) cardiovascular, pulmonary, or cancer (CPC) comorbidity among adults with HIV who smoked. Among 8,581 adults, 4,273 (50%) smoked; 49% of smokers had mental health, and 13% of smokers had a CPC comorbidity. Among smokers, non-Hispanic Black participants had a lower risk for mental health (prevalence ratio [PR]: 0.69; 95% confidence interval [CI] [0.62–0.76]) but a higher risk for CPC (PR: 1.17; 95% CI [0.84–1.62]) comorbidity. Male participants had a lower risk for mental health (PR: 0.88; 95% CI [0.81–0.94]) and CPC (PR: 0.68; 95% CI [0.57–0.81]) comorbidity. All metrics of socioeconomic status were associated with a mental health comorbidity, but only housing status was associated with a CPC comorbidity. We did not find any association with substance use. Gender, socioeconomic factors, and race/ethnicity should inform clinical care and the development of smoking cessation strategies for this population.
Sternomastoid intermuscular approach has better postoperative cosmesis and less neck discomfort than linea alba cervicalis approach in hemithyroidectomy: a randomized clinical trial
Authors: Chen Linghui , He Qiwen , Tian Hedi , Zhu Qinsheng , Shen Yibin , Fang Yun , Zhu Feng , Zhu Lixian , Chen Liang , Pan Jun , Du Yehui , Yan Xiaochuan , Zhang Qijun , Zhou Xueyu , Tian Wen , Wu Yijun
Published: June 2023

Background:

Surgery is still the most important treatment method for thyroid cancer. The classic linea alba cervicalis approach caused obvious neck scarring. This study explored an alternative open operative approach with concealed incision for hemithyroidectomy, and demonstrated whether it was non-inferior to traditional approach in postoperative complications and operation efficiency.

Methods:

Patients (n=220) from November 2019 to November 2020 willing to undergo hemithyroidectomy because of differentiated thyroid cancer were randomly divided into the sternocleidomastoid intermuscular approach (SMIA) group (n=110), and the linea alba cervicalis approach (LACA) group (n=110). The incidence of postoperative complications within 3 months and operation efficiency indicator R0 resection rate were recorded as primary endpoint, while scar apperance was assessed as secondary endpoint. The data were statistically analyzed.

Results:

The baseline data of these two groups were comparable, with no significant difference (P>0.05). As primary endpoint, R0 resection rate was 100% in both groups. In the 1-month follow-up period, the SMIA group had a lower score for neck discomfort compared with that of the LACA group (1.01±0.1648 vs. 0.5657±0.0976, P=0.0217). The SMIA group’s scar had better results from the observer scar assessment compared to that of the LACA group as secondary endpoint. Within the 3-month follow-up, the total complications were calculated, and it was demonstrated that SMIA was non-inferior to traditional LACA operation (P of non-inferiority=0.0048).

Conclusions:

Compared with LACA group, surgery through the SMIA is safe, effective, and has non-inferior postoperative complications. SMIA can be considered an alternative approach to classic LACA in hemithyroidectomy.
Chronic Pancreatitis and Risk of Atherosclerotic Cardiovascular Disease
Authors: Desai Aakash , Chandan Saurabh , Ramai Daryl , Kaul Vivek , Kochhar Gursimran S.
Published: June 2023

Objectives

Worldwide prevalence of chronic pancreatitis (CP) has risen in recent years, with data suggesting an increased risk of atherosclerotic cardiovascular disease (ASCVD) in these patients. We assessed the incidence and risk of ASCVD in patients with CP.

Methods

We compared the risk of ischemic heart disease, cerebrovascular accident, and peripheral arterial disease between CP and non-CP cohorts after propensity matching of known risk factors of ASCVD using TriNetX, a multi-institutional database. We also evaluated the risk of outcomes of ischemic heart disease including acute coronary syndrome, heart failure, cardiac arrest, and all-cause mortality between CP and non-CP cohorts.

Results

Chronic pancreatitis cohort was also found to have an increased risk of ischemic heart disease (adjusted odds ratio [aOR], 1.08; 95% confidence interval [CI], 1.03–1.12), cerebrovascular accident (aOR, 1.12; 95% CI, 1.05–1.20), and peripheral arterial disease (aOR, 1.17; 95% CI, 1.1–1.24). Chronic pancreatitis patients with ischemic heart disease were also found to have an increased risk of acute coronary syndrome (aOR, 1.16; 95% CI, 1.04–1.30), cardiac arrest (aOR, 1.24; 95% CI, 1.01–1.53), and mortality (aOR, 1.60; 95% CI, 1.45–1.77).

Conclusions

Chronic pancreatitis patients are at a higher risk of ASCVD when compared with the general population, matched for confounding etiological, pharmacological, and comorbid variables.
Characteristics of New Oxygen-Carrying Plasma and Its Application Prospects in the Treatment of Severe Acute Pancreatitis
Authors: Song Jingyu , Pan Xinting , Li Junjie , Hu Xiaomin , Yin Wen
Published: June 2023

Oxygen-carrying plasma, a new type of colloid substitute, is composed of hydroxyethyl starch and acellular hemoglobin-based oxygen carriers. It can supplement colloidal osmotic pressure and rapidly improve the body's oxygen supply. The resuscitation effect of the new oxygen-carrying plasma in animal shock models is better than that of hydroxyethyl starch or hemoglobin-based oxygen carriers alone. It can reduce the histopathological damage and mortality associated with severe acute pancreatitis, and it is expected to become an interesting treatment method for severe acute pancreatitis. This article reviews the characteristics of the new oxygen-carrying plasma, its role in fluid resuscitation, and its application prospects in the treatment of severe acute pancreatitis.
Survival and Prognostic Factors in Patients With Pancreatic Colloid Carcinoma Compared With Pancreatic Ductal Adenocarcinoma
Authors: Khalil Lana , Huang Zhonglu , Zakka Katerina , Jiang Renjian , Penley McKenna , Alese Olatunji B. , Shaib Walid L. , Wu Christina , Behera Madhusmita , Reid Michelle D. , El-Rayes Bassel F. , Akce Mehmet
Published: June 2023

Objectives

Colloid carcinoma (CC) is a rare subtype of pancreatic carcinoma. The aims of the study are to characterize the clinicopathological features and to evaluate the overall survival (OS) of patients with CC.

Methods

Patients diagnosed with pancreatic CC and pancreatic ductal adenocarcinoma (PDAC) between 2004 and 2016 were identified from the National Cancer Database using International Classification of Disease-O-3 morphology (8480/3 and 8140/3) and topography (C25) codes. Kaplan-Meier analysis and Cox proportional hazards models were used to analyze OS.

Results

Fifty-six thousand eight hundred forty-six patients were identified. A total of 2430 patients (4.3%) were diagnosed with pancreatic CC. Males constituted 52.8% of CC and 52.2% of PDAC. Colloid carcinoma presented with pathological stage I disease more often (16.7% vs 5.9%) and stage IV disease less often (42.1% vs 52.4%) than PDAC (P < 0.001). Stage I CC received chemotherapy (36.0% vs 59.4%) and neoadjuvant chemotherapy (4.4% vs 14.2%) less often compared with PDAC (P < 0.001). Statistically significant improved OS was seen among stage I, II, and IV CC compared with PDAC.

Conclusions

Pancreatic CC presented as stage I disease more often compared with PDAC. Neoadjuvant chemotherapy was administered more often in stage I PDAC compared with CC. Colloid carcinoma had improved OS compared with PDAC among all stages except stage III.
Can We Rely on Resting Metabolic Rate Equations? Large Variance in Crohn Disease Pediatric Patients
Authors: Marderfeld Luba , Guz Mark Anat , Biran Neta , Shamir Raanan
Published: June 2023

Objectives:

Inadequate caloric intake is common in Crohn disease (CD) and nutrition support plays an important role in remission induction and in meeting nutritional needs. For nutritional planning, determining resting metabolic rate (RMR) is essential in pediatric patients with CD.

Study Aim:

To measure RMR in CD pediatric patients using indirect calorimetry, and compare it with estimated RMR (eRMR) calculated by Schofield equation.

Methods:

Children with CD treated in a tertiary pediatric inflammatory bowel disease center in Israel participated in the cross-sectional study. At study visits, weight, height, clinical and laboratory assessments, bioelectrical impedance, and RMR measured by indirect calorimetry were done. Additionally, disease severity was determined by the Pediatric Crohn Disease Activity Index and eRMR was calculated using the Schofield equation. The ratio of the measured RMR to eRMR was performed in addition to the Spearman correlation test.

Results:

The study group included 73 children (49 boys) with mean age of 13.9 ± 2.3 years. Children with moderate or severe disease had lower weight for age z score, lower BMI-z, and lower RMR compared to children with mild disease. However, when RMR was adjusted for fat free mass (n = 50), the association between RMR and disease severity disappeared. Variance in RMR was high between subjects.

Conclusions:

Our data suggest that the Schofield equation is inadequate for determining RMR in pediatric CD and that RMR should be measured to guarantee the most appropriate nutritional intervention.
Scalable Strategies to Increase Efficiency and Augment Public Health Activities During Epidemic Peaks
Authors: Pasquale Dana K. , Welsh Whitney , Olson Andrew , Yacoub Mark , Moody James , Barajas Gomez Brisa A. , Bentley-Edwards Keisha L. , McCall Jonathan , Solis-Guzman Maria Luisa , Dunn Jessilyn P. , Woods Christopher W. , Petzold Elizabeth A. , Bowie Aleah C. , Singh Karnika , Huang Erich S.
Published: June 2023

Objective:

Scalable strategies to reduce the time burden and increase contact tracing efficiency are crucial during early waves and peaks of infectious transmission.

Design:

We enrolled a cohort of SARS-CoV-2-positive seed cases into a peer recruitment study testing social network methodology and a novel electronic platform to increase contact tracing efficiency.

Setting:

Index cases were recruited from an academic medical center and requested to recruit their local social contacts for enrollment and SARS-CoV-2 testing.

Participants:

A total of 509 adult participants enrolled over 19 months (384 seed cases and 125 social peers).

Intervention:

Participants completed a survey and were then eligible to recruit their social contacts with unique “coupons” for enrollment. Peer participants were eligible for SARS-CoV-2 and respiratory pathogen screening.

Main Outcome Measures:

The main outcome measures were the percentage of tests administered through the study that identified new SARS-CoV-2 cases, the feasibility of deploying the platform and the peer recruitment strategy, the perceived acceptability of the platform and the peer recruitment strategy, and the scalability of both during pandemic peaks.

Results:

After development and deployment, few human resources were needed to maintain the platform and enroll participants, regardless of peaks. Platform acceptability was high. Percent positivity tracked with other testing programs in the area.

Conclusions:

An electronic platform may be a suitable tool to augment public health contact tracing activities by allowing participants to select an online platform for contact tracing rather than sitting for an interview.
Transcriptomic analysis of granulosa cells in patients with endometriosis-related infertility: identification of potential molecular mechanisms
Authors: Zhang Jian , Zhang Yu , Luo Jia-Li , Yu Lin , Gao Min-Zhi , Sun Zhao-Gui
Published: June 2023

Objective:

To investigate the impact of endometriosis on granulosa cell function and elucidate the molecular mechanisms involved.

Methods:

RNA sequencing, differential expression analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, gene set enrichment analysis, protein-protein interaction analysis, and RT-qPCR were employed to assess the effects of endometriosis on granulosa cell function.

Results:

The results revealed significant differences in gene expression between the endometriosis and control groups, including genes related to immune regulatory functions and ferroptosis. Hub gene modules and hub genes were identified, including those related to cell cycle and immune and inflammatory pathways. RT-qPCR revealed significant up-regulation of the hub genes CCL3 and IL1B in granulosa cells of patients with endometriosis.

Conclusion:

The results of RNA sequencing demonstrated that endometriosis induces significant transcriptional alterations in granulosa cells of affected patients. These findings provide important insights into the diagnosis and treatment of endometriosis and highlight the importance of further investigation of CCL3 and IL1B as potential biomarkers for endometriosis.
Stromal cell decidualization and embryo implantation: a vulnerable step leading to successful pregnancy
Authors: Jiang Luhan , Fernando Sudini R. , Kodithuwakku Suranga P. , Cao Dandan , Yeung William S. B. , Lee Kai-Fai
Published: June 2023

Endometrial stromal cell decidualization is a crucial step in endometrial remodeling during pregnancy. Decidualization is controlled by orchestrated ovarian hormones, followed by the activation of various downstream signaling pathways. Accumulating evidence has shown multiple functions of decidualized endometrial stromal cells during embryo implantation, including tissue remodeling, antioxidative stress, angiogenesis, and immune tolerance. The distinct secretomes of decidualized stromal cells also reveal their intensive interactions with epithelial, endothelial, and immune cells. However, aberrant decidualization leads to pregnancy failures, such as recurrent pregnancy loss and repeated implantation failure. This review aimed to provide an overview of the molecular mechanisms underlying the divergent functions of decidualized endometrial stromal cells and their potential clinical applications. Moreover, the use of single-cell RNA sequencing data further enhances our understanding of these biological processes. This review discusses decidualization-related signaling pathways that serve as potential therapeutic targets for treating implantation failure in in vitro fertilization and provides novel approaches to investigate the underlying causes of female infertility.
Critical appraisal of the emergency management of cardiac conditions during pregnancy in an Egyptian tertiary unit: Newness in paradigms
Authors: Mahmoud Mohamed , Elhalim Abd Elhalim Mohamed Abd , Ellaban Mostafa , Saleh Mohamed , Ali Hamdi Mohamed , Abdalla Khaled M , Eldeib Moustafa , Faheem Ahmed Ali , Almarghany Alsayed , Samy Mohammed , Zahran Al Hussein , Ali Ahmed Ali , Ali Medhat
Published: June 2023

The relevance of the multidisciplinary team of cardiology, obstetrics, and clinical pathology has increased and now demands cooperation to manage cardiovascular diseases during pregnancy. A diverse and skilled team (the "pregnancy heart team") should ideally be included early in the pregnant woman's care when she comes with an acute cardiovascular issue during gestation. Acute cardiac disorders that may develop during pregnancy include heart failure (HF), arrhythmias, coronary artery disease, aortic and thromboembolic events, and mechanical heart valves. Cardiovascular disease is the leading cause of pregnancy-related fatalities in underdeveloped countries [1]. Increasing maternal age and concomitant conditions increased maternal death rates. A multidisciplinary cardio-obstetrics-clinical pathology team must provide preconception counselling to women with pre-existing cardiac issues or a history of preeclampsia. To reduce maternal morbidity and mortality during pregnancy and in the first year after birth, this team must be included as soon as possible. The basics of cardiovascular disease during pregnancy should be understood by both cardiovascular and primary care professionals. The diagnosis and emergency therapy of severe cardiovascular disease during pregnancy at Al-Azhar University, a tertiary care facility in Egypt, are covered in this scholarly research, which also highlights the novelty of paradigms for managing such situations in low-resource countries.
The SHELTER Trial of Transplanting Hepatitis C Virus–Infected Lungs Into Uninfected Recipients
Authors: Reese Peter P. , Diamond Joshua M. , Goldberg David S. , Potluri Vishnu , Prenner Stacey , Blumberg Emily A. , Van Deerlin Vivianna M. , Reddy K. Rajender , Mentch Heather , Hasz Richard , Woodards Ashley , Gentile Caren , Smith Jennifer , Bermudez Christian , Crespo Maria M.
Published: June 2023

Background.

SHELTER is a trial of transplanting lungs from deceased donors with hepatitis C virus (HCV) infection into HCV-negative candidates (sponsor: Merck; NCT03724149). Few trials have reported outcomes using thoracic organs from HCV-RNA+ donors and none have reported quality of life (QOL).

Methods.

This study is a single-arm trial of 10 lung transplants at a single center. Patients were included who were between 18 and 67 y of age and waitlisted for lung-only transplant. Patients were excluded who had evidence of liver disease. Primary outcome was HCV cure (sustained virologic response 12 wk after completing antiviral therapy). Recipients longitudinally reported QOL using the validated RAND-36 instrument. We also applied advanced methods to match HCV-RNA+ lung recipients to HCV-negative lung recipients in a 1:3 ratio at the same center.

Results.

Between November 2018 and November 2020, 18 patients were consented and opted-in for HCV-RNA+ lung offers in the allocation system. After a median of 37 d (interquartile range [IQR], 6–373) from opt-in, 10 participants received double lung transplants. The median recipient age was 57 y (IQR, 44–67), and 7 recipients (70%) had chronic obstructive pulmonary disease. The median lung allocation score at transplant was 34.3 (IQR, 32.7–86.9). Posttransplant, 5 recipients developed primary graft dysfunction grade 3 on day 2 or 3, although none required extracorporeal membrane oxygenation. Nine patients received elbasvir/grazoprevir, whereas 1 patient received sofosbuvir/velpatasvir. All 10 patients were cured of HCV and survived to 1 y (versus 83% 1-y survival among matched comparators). No serious adverse events were found to be related to HCV or treatment. RAND-36 scores showed substantial improvement in physical QOL and some improvement in mental QOL. We also examined forced expiratory volume in 1 s—the most important lung function parameter after transplantation. We detected no clinically important differences in forced expiratory volume in 1 s between the HCV-RNA+ lung recipients versus matched comparators.

Conclusions.

SHELTER adds important evidence regarding the safety of transplanting HCV-RNA+ lungs into uninfected recipients and suggests QOL benefits.
Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation
Authors: Heiple Zach , Huie Jonathan M. , Medeiros Aline P. M. , Hart Pamela B. , Goatley Christopher H. R. , Arcila Dahiana , Miller Elizabeth Christina
Published: June 2023

Almost nothing is known about the diets of bathypelagic fishes, but functional morphology can provide useful tools to infer ecology. Here we quantify variation in jaw and tooth morphologies across anglerfishes (Lophiiformes), a clade spanning shallow and deep-sea habitats. Deep-sea ceratioid anglerfishes are considered dietary generalists due to the necessity of opportunistic feeding in the food-limited bathypelagic zone. We found unexpected diversity in the trophic morphologies of ceratioid anglerfishes. Ceratioid jaws span a functional continuum ranging from species with numerous stout teeth, a relatively slow but forceful bite, and high jaw protrusibility at one end (characteristics shared with benthic anglerfishes) to species with long fang-like teeth, a fast but weak bite and low jaw protrusibility at the other end (including a unique ‘wolftrap’ phenotype). Our finding of high morphological diversity seems to be at odds with ecological generality, reminiscent of Liem's paradox (morphological specialization allowing organisms to have broader niches). Another possible explanation is that diverse ceratioid functional morphologies may yield similar trophic success (many-to-one mapping of morphology to diet), allowing diversity to arise through neutral evolutionary processes. Our results highlight that there are many ways to be a successful predator in the deep sea.
ViewShedR: a new open-source tool for cumulative, subtractive and elevated line-of-sight analysis
Authors: Arnon Eitam , Uzan Assaf , Handel Michal , Cain Shlomo , Toledo Sivan , Spiegel Orr
Published: June 2023

Many environmental and ecological studies require line of sight (LOS) and/or viewshed analyses. While tools for performing these analyses from digital elevation models (DEMs) are widespread, they are either too restrictive, inaccessible or pricey and difficult to use. This methodological gap is potentially imperative for scholars using solutions like telemetry tracking systems or spatial ecology landscape mapping. Here we present ViewShedR—a free, open-source and intuitive graphical user-interface application for performing LOS calculations, including cumulative, subtractive (areas covered by towers A + B or by A but not by B, respectively), and elevated-target analyses. ViewShedR is implemented in the widely used R environment, thus facilitating usage and further modification by end-users. We provide two working examples for ViewShedR in the context of permanent animal-tracking systems requiring simultaneous tag-detection by multiple towers (receivers): first, the ATLAS system for terrestrial animals in the Harod Valley, Israel; and second, an acoustic telemetry array for marine animals in the Dry Tortugas, Florida. ViewShedR allowed effective tower deployment and finding partially detected tagged animals in the ATLAS system. Similarly, it allowed us to identify reception shadows cast by islands in the marine array. We hope ViewShedR will facilitate deployment of tower arrays for tracking, communication networks and other ecological applications.
Gordonia sputi-associated bloodstream infection in a renal transplant patient with chronic indwelling central venous catheter: a case report and literature review
Authors: Lo Calvin Ka-Fung , Broderick Conor , Stefanovic Aleksandra , Connors William , Murray Melanie
Published: June 2023

Introduction. Although rare, human infections caused by

Gordonia

spp. have been reported, especially within the immunocompromised population and those with long-term indwelling devices. We report a case of

Gordonia

spp. bacteraemia in a renal transplant patient and present a literature review on microbiological identification methods of this organism.

Case Presentation. A 62-year-old female renal transplant recipient admitted to hospital with a 2-month history of dry cough and fevers occurring weekly when receiving electrolyte replacement infusions via a Groshong line. Over 2 weeks, blood cultures repeatedly isolated a Gram-positive bacillus solely in aerobic bottles, and this was initially reported as

Rhodococcus

spp. by the local microbiology laboratory. Chest computed tomography (CT) showed multiple ground-glass lung opacities suggestive of septic pulmonary emboli. As central line-associated bloodstream infection was suspected, empirical antibiotics were initiated and the Groshong line was removed. The Gram-positive bacillus was later confirmed by the reference laboratory as

Gordonia sputi

via 16S rRNA sequencing. Vancomycin and ciprofloxacin for a duration of 6 weeks were completed as targeted antimicrobial therapy. After treatment, the patient remained symptom-free with marked improvement on repeat CT chest imaging.

Conclusion. This case illustrates the challenges surrounding identification of

Gordonia

spp. and other aerobic actinomycetes. 16S rRNA gene sequencing may be a preferred identification method, especially when initial workup of a weakly acid-fast organism fails to make an identification or shows discrepant results using traditional diagnostic modalities.
Regeneration leads to global tissue rejuvenation in aging sexual planarians
Authors: Dai Xiaoting , Li Xinghua , Pletcher Scott , Paris David , Kruglyak Leonid , Sobota Jacob , Guo Longhua
Published: June 2023

An ability to delay aging—or to reverse the negative effects of aging—could prevent age-related disease and greatly enhance quality of life in old age. However, whether it is possible to globally reverse the physiological effects of aging in order to extend healthspan is unknown. The freshwater planarianSchmidtea mediterraneahas been considered “immortal” due to its exceptional tissue regeneration capabilities. Here, we report that a sexually reproducing lineage ofS. mediterraneaexhibits age-associated physiological decline 12 months after birth. Age-associated changes include alterations in sensory organs, loss of neurons and muscle, loss of fertility, and impaired motility, but no reduction in stem cells at the age of 3 years. Differential gene expression analysis, comparing young and old planarian cells, furthermore revealed cell-type-specific changes in transcription as well as changes in classical aging pathways (e.g., insulin signaling). Remarkably, amputation followed by regeneration of lost tissues led to a global reversal of these age-associated changes. Older individuals that underwent regeneration showed restored youthful patterns of gene expression, stem cell states, tissue composition and rejuvenation of whole-animal physiology. Our work reveals a naturally evolved solution to age reversal in planaria that may provide insights into anti-aging strategies in humans.
HemorrhageEvaluation AndDetectorSystem forUnderservedPopulations:HEADS UP
Authors: Salman Saif , Gu Qiangqiang , Dherin Benoit , Reddy Sanjana , Vanderboom Patrick , Sharma Rohan , Lancaster Lin , Tawk Rabih , Freeman William David
Published: June 2023

Introduction

Intracerebral hemorrhage (ICH) is the second most common cause of stroke and remains the second leading cause of disability impacting underserved areas. Since 2015, there has been a paradigm shift in managing ischemic stroke through applying AI and ML. However, ICH patients lack such protocol.

Objective

To create a rapid, cloud-based, and deployable ML method to detect ICH potentially across the Mayo Clinic enterprise then expand to involve underserved areas.

Methods

We utilized RSNA dataset for ICH. We made four total iterations using Google Cloud Vertex AutoML. We trained an AutoML model with 2,000 images followed by 6,000 images from both ICH positive and negative classes. Pixel values were measured by the Hounsfield units presenting a width of 80 Hounsfield and a level of 40 Hounsfield as the bone window. This was followed by a more detailed image preprocessing approach by combining the pixel values from each of the brain, subdural, and soft tissue window-based grayscale images into R(red)G(green)B(blue)-channel images to boost the binary ICH classification performance. Four experiments with AutoML were applied to study the impacts of training sample size and image preprocessing on model performance.

Results

Out of the four AutoML experiments, the best-performing model achieved a 95.8% average precision, 91.4% precision, and 91.4% recall. Based on this analysis, our binary ICH classifierHEADS UPis both accurate and performant.

Conclusion

HEADS UP, is a rapid, cloud-based, deployable ML method to detect ICH. This tool can help expedite the care of patients with ICH in resource-limited hospitals.
The Maudsley 3-item visual analogue scale (M3VAS): Longitudinal validation of a new measure to capture depression
Authors: Middag Maria Elena , Silman Daniel , Cleare Anthony , Young Allan , Carter Ben , Strawbridge Rebecca
Published: June 2023

The existing ‘gold standard’ assessments of depression suffer various issues, which include the evaluation of constructs extraneous to the core symptoms of the illness, and low sensitivity to change over time. Members of our team developed a new, simple visual analogue scale that aims to address these issues (M3VAS). Initial validation of the scale demonstrated good internal consistency and convergent validity. Still, we have not yet investigated how well it assesses changes in the severity of depressive symptoms over time. This project will analyse data from a longitudinal study (Hampsey et al., 2022), aiming to ascertain whether the M3VAS is sensitive to change i.e., how well it detects either a worsening or improvement of symptoms over a number of weeks (repeated measures). Validating this scale’s longitudinal validity could provide a better way for future longitudinal (observational and interventional) studies to identify changes in the severity of depressive illness.
Risk factors for severe COVID-19 outcomes: a study of immune-mediated inflammatory diseases, immunomodulatory medications, and comorbidities in a large US healthcare system
Authors: Wei Qi , Mease Prof Philip J. , Chiorean Michael , Iles-Shih Lulu , Matos Wanessa F. , Baumgartner Andrew , Molani Sevda , Hwang Yeon Mi , Belhu Basazin , Ralevski Alexandra , Hadlock Jennifer
Published: June 2023

Background

COVID-19 outcomes, in the context of immune-mediated inflammatory diseases (IMIDs), are incompletely understood. Reported outcomes vary considerably depending on the patient population studied. It is essential to analyse data for a large population, while considering the effects of the pandemic time period, comorbidities, long term use of immunomodulatory medications (IMMs), and vaccination status.

Methods

In this retrospective case-control study, patients of all ages with IMIDs were identified from a large U.S. healthcare system. COVID-19 infections were identified based on SARS-CoV-2 NAAT test results. Controls without IMIDs were selected from the same database. Severe outcomes were hospitalisation, mechanical ventilation (MV), and death. We analysed data from 1 March 2020 to 30 August 2022, looking separately at both pre-Omicron and Omicron predominant periods. Factors including IMID diagnoses, comorbidities, long term use of IMMs, and vaccination and booster status were analysed using multivariable logistic regression (LR) and extreme gradient boosting (XGB).

Findings

Out of 2 167 656 patients tested for SARS-CoV-2, there were 290 855 with confirmed COVID-19 infection: 15 397 patients with IMIDs and 275 458 controls (patients without IMIDs). Age and most chronic comorbidities were risk factors for worse outcomes, whereas vaccination and boosters were protective. Patients with IMIDs had higher rates of hospitalisation and mortality compared with controls. However, in multivariable analyses, few IMIDs were rarely risk factors for worse outcomes. Further, asthma, psoriasis and spondyloarthritis were associated with reduced risk. Most IMMs had no significant association, but less frequently used IMM drugs were limited by sample size. XGB outperformed LR, with the AUROCs for models across different time periods and outcomes ranging from 0·77 to 0·92.

Interpretation

For patients with IMIDs, as for controls, age and comorbidities were risk factors for worse COVID-19 outcomes, whereas vaccinations were protective. Most IMIDs and immunomodulatory therapies were not associated with more severe outcomes. Interestingly, asthma, psoriasis and spondyloarthritis were associated with less severe COVID-19 outcomes than those expected for the population overall. These results can help inform clinical, policy and research decisions.

Funding

Pfizer, Novartis, Janssen, NIH

MeSH

D001327, D000086382, D025241, D012306, D000071069
Reference genome of the bicolored carpenter ant,Camponotus vicinus
Authors: Ward Philip S. , Cash Elizabeth I. , Ferger Kailey , Escalona Merly , Sahasrabudhe Ruta , Miller Courtney , Toffelmier Erin , Fairbairn Colin , Seligmann William , Shaffer H. Bradley , Tsutsui Neil D.
Published: June 2023

Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, C. vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, CA, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest.
The genome sequence of the Montseny horsehair worm,Gordionus montsenyensissp. nov., a key resource to investigate Ecdysozoa evolution
Authors: Eleftheriadi Klara , Guiglielmoni Nadège , Salces-Ortiz Judit , Vargas-Chavez Carlos , Martínez-Redondo Gemma I. , Gut Marta , Flot Jean-François , Schmidt-Rhaesa Andreas , Fernández Rosa
Published: June 2023

Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. They are one of the less scientifically studied animal phyla, and many aspects of their biology and evolution are still unknown, partially due to the lack of genomic resources for this phylum. As part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity, we present the taxonomic description and chromosome-level genome assembly of a newly described species of Nematomorpha (Gordionus montsenyensisSchmidt-Rhaesa & Fernández sp. nov.). The final assembly has a total length of 288 Mb in 396 scaffolds with an N50 of 64.4 Mb, 97% of which is scaffolded into 5 pseudochromosomes. The circular mitochondrial genome was also assembled into a 15-kilobases sequence. Gene annotation predicted 10,320 protein-coding genes in the nuclear genome. In this study, we contribute a key genomic resource to not only explore the evolution of Ecdysozoa, but also to further our understanding on the genomic basis of parasitic lifestyles. In addition, we describe a species new to science from this enigmatic animal phyla.
Transfemoral limb loss modestly increases the metabolic cost of optimal control simulations of walking
Authors: Miller Ross H. , Bell Elizabeth M. , Esposito Elizabeth Russell
Published: June 2023

Unlike the case of transtibial limb loss, high-functioning military service members with transfemoral limb loss have a high metabolic cost of walking compared to able-bodied peers. In transtibial limb loss, computer simulations suggest that the maintenance of muscle strength between pre- and post-limb loss can maintain the pre-limb loss metabolic cost. Here we performed optimal control simulations of walking with and without transfemoral limb loss to determine if transfemoral limb lossper seincreases the metabolic cost of walking. OpenSim Moco was used to generate optimal control simulations of walking in 15 virtual subjects that minimized the weighted sum of (i) deviations from average able-bodied gait mechanics and (ii) the gross metabolic cost of walking, pre-limb loss in models with two intact biological limbs, and post-limb loss with one of the limbs replaced by a transfemoral prosthesis. No other changes were made to the model. Metabolic cost post-limb loss increased by 0.7-9.3% (p< 0.01) depending on whether cost was scaled by total body mass or biological body mass and on whether the prosthetic knee was passive or non-passive. The post-limb loss model had numerous features that predisposed it to low metabolic cost. These results suggest that transfemoral limb lossper seincreases the metabolic cost of walking, but that the large differences above able-bodied peers of ∼20% or more in most gait analysis experiments may be avoidable, even when minimizing deviations from able-bodied gait mechanics.
Intraspecific variation in the placement of campaniform sensilla on the wings of the hawkmothManduca sexta
Authors: Stanchak Kathryn E. , Deora Tanvi , Weber Alison I. , Hickner Michelle K. , Moalin Abna , Abdalla Laila , Daniel Thomas L. , Brunton Bingni W.
Published: June 2023

Flight control requires active sensory feedback, and insects have many sensors that help them estimate their current locomotor state, including campaniform sensilla, which are mechanoreceptors that sense strain resulting from deformation of the cuticle. Campaniform sensilla on the wing detect bending and torsional forces encountered during flight, providing input to the flight feedback control system. During flight, wings experience complex spatio-temporal strain patterns. Because campaniform sensilla detect only local strain, their placement on the wing is presumably critical for determining the overall representation of wing deformation; however, how these sensilla are distributed across wings is largely unknown. Here, we test the hypothesis that campaniform sensilla are found in stereotyped locations across individuals ofManduca sexta, a hawkmoth. We found that although campaniform sensilla are consistently found on the same veins or in the same regions of the wings, their total number and distribution can vary extensively. This suggests that there is some robustness to variation in sensory feedback in the insect flight control system. The regions where campaniform sensilla are consistently found provide clues to their functional roles, although some patterns might be reflective of developmental processes. Collectively, our results on intraspecific variation in campaniform sensilla placement on insect wings will help reshape our thinking on the utility of mechanosensory feedback for insect flight control and guide further experimental and comparative studies.
Chemically-induced epileptic seizures in zebrafish: a systematic review
Authors: Chitolina Rafael , Gallas-Lopes Matheus , Reis Carlos G. , Benvenutti Radharani , Stahlhofer-Buss Thailana , Calcagnotto Maria Elisa , Herrmann Ana P. , Piato Angelo
Published: June 2023

The use of zebrafish as a model organism is gaining evidence in the field of epilepsy as it may help to understand the mechanisms underlying epileptic seizures. As zebrafish assays became popular, the heterogeneity between protocols increased, making it hard to choose a standard protocol to conduct research while also impairing the comparison of results between studies. We conducted a systematic review to comprehensively profile the chemically-induced seizure models in zebrafish. Literature searches were performed in PubMed, Scopus and Web of Science, followed by a two-step screening process based on inclusion/exclusion criteria. Qualitative data were extracted and a sample of 100 studies was randomly selected for risk of bias assessment. Out of the 1058 studies identified after removing duplicates, 201 met the inclusion criteria. We found that the most common chemoconvulsants used in the reviewed studies were pentylenetetrazole (n = 180), kainic acid (n = 11), and pilocarpine (n = 10), which increase seizure severity in a dose-dependent manner. The main outcomes assessed were seizure scores and locomotion. Significant variability between the protocols was observed for administration route, duration of exposure, and dose/concentration. Of the studies subjected to risk of bias assessment, most were rated as low risk of bias for selective reporting (94%), baseline characteristics of the animals (67%), and blinded outcome assessment (54%). Randomization procedures and incomplete data were rated as unclear in 81% and 68% of the studies, respectively. None of the studies reported the sample size calculation. Overall, these findings underscore the need for improved methodological and reporting practices to enhance reproducibility and reliability of zebrafish models for studying epilepsy. Our study offers a comprehensive overview of the current state of chemically-induced seizure models in zebrafish, highlighting the common chemoconvulsants used and the variability in protocol parameters. This may be particularly valuable to researchers interested in understanding the underlying mechanisms of epileptic seizures and screening potential drug candidates in zebrafish models.

HIGHLIGHTS

- We systematically reviewed the effects of chemically-induced seizures in zebrafish;

- PTZ is the most used epileptic seizure inducer in zebrafish;

- More than 50% of the studies fail to report data such as outlier exclusion criteria and sample size estimation;

- The results showed a need for better standardization of protocols.
Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones
Authors: Ianevski Aleksandr , Nader Kristen , Bulanova Daria , Giri Anil K , Ruokoranta Tanja , Kuusanmäki Heikki , Ikonen Nemo , Sergeev Philipp , Vähä-Koskela Markus , Vähärautio Anna , Kontro Mika , Porkka Kimmo , Heckman Caroline A. , Wennerberg Krister , Aittokallio Tero
Published: June 2023

Intratumoral cellular heterogeneity necessitates multi-targeting therapies for improved clinical benefits in patients with advanced malignancies. However, systematic identification of patient-specific treatments that selectively co-inhibit cancerous cell populations poses a combinatorial challenge, since the number of possible drug-dose combinations vastly exceeds what could be tested in scarce patient cells. Here, we developed scTherapy, a machine learning model that leverages single-cell transcriptomic profiles to prioritize multi-targeting treatment options for individual patients with hematological cancers or solid tumors.