bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesozooplankton biodiversity, vertical assemblages, and diel migration in the western tropical Pacific Ocean revealed by eDNA metabarcoding and morphological methods
Authors: Feng Yunzhi , Sun Dong , Shao Qianwen , Fang Chen , Wang Chunsheng 
Published: October 2022

Zooplankton plays a crucial role in marine ecosystems. However, due to issues with morphological identification and sampling methods, knowledge of their biodiversity and community structure in the vast pelagic zone of the western tropical Pacific Ocean is still limited compared with other areas in the North Pacific Ocean. In this study, we used environmental DNA (eDNA) metabarcoding and morphological identification approaches to investigate mesozooplankton’s biodiversity and vertical assemblages in the western tropical Pacific Ocean from the surface to 1000 m deep. Two different barcodes were used in metabarcoding: mitochondrial cytochrome oxidase I (COI) and small subunit ribosomal RNA genes (18S). Our results showed that eDNA metabarcoding revealed 2-4 times more medusae taxa than morphological processing. Both methods detected that small copepod species were dominant in the community and six of the top-10 most abundant copepod genera overlapped. Morphological results showed that mesozooplankton communities were classified into three groups: epipelagic (0–200 m), upper mesopelagic (200-500 m), and lower mesopelagic (500–1000 m). And eDNA results showed distinct vertical variations of mesozooplankton communities within the epipelagic. Both methods showed that the dominant genera Clausocalanus, Paracalanus, and Calocalanus exhibited diel patterns in relative abundance, demonstrating that the eDNA method can capture diel vertical migration (DVM) signals of copepods. Overall, our results indicate that eDNA metabarcoding is an effective and efficient tool for the study and monitoring of mesozooplankton diversity and vertical assemblages in the open sea.
Rhodolith beds and their onshore transport in Fuerteventura Island (Canary Archipelago, Spain)
Authors: Rebelo Ana Cristina , Martín-González Esther , Melo Carlos S. , Johnson Markes E. , González-Rodríguez Alberto , Galindo Inés , Quartau Rui , Baptista Lara , Ávila Sérgio P. , Rasser Michael W. 
Published: October 2022

Rhodoliths occur extensively around the shores of Fuerteventura Island in the Canary Archipelago, with Lithothamnion cf. corallioides being the most prominent species. A large number of rhodoliths end up washed onshore, the debris from which contributes to the formation of sediments constituting modern beaches. In a previous study by one of the co-authors (MEJ), the northern coast of Fuerteventura was shown to comprise various types of rhodolith deposits such as beach, platform overwash, tidal pools, coastal dunes, and others. An extraordinary example of stranded rhodoliths is located near Caleta del Bajo de Mejillones, approximately 3 km west of Corralejo, on the north coast of the island. The deposit forms a supratidal beach 120 m long and 10 m wide that sits above the landward termination of an extensive wave-cut platform eroded in basalt and exposed at low tide to a width of 130 m perpendicular to shore. Here, rhodoliths are very small (&lt;3 cm) resembling popcorn, and the locality is known as the “Popcorn Beach”. Other examples are berms up to 150 m long and 9 m wide at Caleta del Bajo de Mejillones, or an exposed beach at Playa del Hierro with an area of more than 1500 m2 covered entirely of very coarse rhodolith sand. Extensive living rhodolith beds were found at a water depth of 22 m.
Pharmacogenes that demonstrate high association evidence according to CPIC, DPWG, and PharmGKB
Authors: Alshabeeb Mohammad A. , Alyabsi Mesnad , Aziz Mohammad A. , Abohelaika Salah 
Published: October 2022

BackgroundDifferent levels of evidence related to the variable responses of individuals to drug treatment have been reported in various pharmacogenomic (PGx) databases. Identification of gene-drug pairs with strong association evidence can be helpful in prioritizing the implementation of PGx guidelines and focusing on a gene panel. This study aimed to determine the pharmacogenes with the highest evidence-based association and to indicate their involvement in drug-gene interactions.MethodologyThe publicly available datasets CPIC, DPWG, and PharmGKB were selected to determine the pharmacogenes with the highest drug outcome associations. The upper two levels of evidence rated by the three scoring methods were specified (levels A–B in CPIC, 3–4 in DPWG, or 1–2 levels in PharmGKB). The identified pharmacogenes were further ranked in this study based on the number of medications they interacted with.ResultsFifty pharmacogenes, with high to moderately high evidence of associations with drug response alterations, with potential influence on the therapeutic and/or toxicity outcomes of 152 drugs were identified. CYP2D6, CYP2C9, CYP2C19, G6PD, HLA-B, SLCO1B1, CACNA1S, RYR1, MT-RNR1, and IFNL4 are the top 10 pharmacogenes, where each is predicted to impact patients' responses to ≥5 drugs.ConclusionThis study identified the most important pharmacogenes based on the highest-ranked association evidence and their frequency of involvement in affecting multiple drugs. The obtained data is useful for customizing a gene panel for PGx testing. Identifying the strength of scientific evidence supporting drug-gene interactions aids drug prescribers in making the best clinical decision.
One-stage laparoscopy combined with resectoscope in the treatment of huge bladder diverticulum, multiple stones in diverticulum, multiple stones in bladder and benign prostatic hyperplasia: A case report
Authors: Zhengqiang Wan , Yinglei Wang , Cheng Li , Dongbing Zheng 
Published: October 2022

BackgroundBladder diverticulum is due to the abnormal arrangement of congenital bladder wall muscle fibers, weak limitations, combined with lower urinary tract obstruction, increased intravesical pressure, and protruding between the self-separated detrusor muscle bundles of the bladder wall. Giant bladder diverticulum refers to 10*8 cm or diverticulum over 150 ml in volume.Case summaryAn 80-year-old male patient was admitted to our hospital on August 14, 2020, the preoperative diagnosis was: bladder diverticulum, bladder diverticulum calculi, multiple bladder stones and prostatic hyperplasia. On August 18, 2020, one-stage laparoscopic bladder diverticulectomy + diverticulum neck incision for stone removal + cystopuncture fistula + transurethral bladder stone removal + transurethral resection of the prostate (TURP) under general anesthesia. First, the bladder diverticulum was separated under laparoscopy, the diverticulum was incised, the diverticulum calculi were taken out, and then the diverticulum was completely removed, and the neck of the diverticulum was extended by 1.5 cm, and the large calculus of about 2.7*3.6 cm was completely removed, and then cystostomy + transurethral Bladder stone removal + TURP. There was no bleeding from the bladder suture during the operation. 200 ml of urine was drained from the extraperitoneal drainage tube, and 20 ml of urine was drained from the abdominal drainage tube during the operation, the urination is smooth, and the general condition can be discharged. The patient’s general condition is good after follow-up.ConclusionOne-stage laparoscopic treatment of bladder diverticulectomy + diverticulum neck incision for stone extraction + cystopuncture fistula + transurethral bladder stone extraction + TURP surgery. There is no report at home and abroad, which can provide diagnosis and treatment ideas and surgical methods for urological colleagues to deal with such diseases.
Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum
Authors: Kok Nienke A. , Peker Nilay , Schuele Leonard , de Beer Jessica L. , Rossen John W. A. , Sinha Bhanu , Couto Natacha 
Published: October 2022

Identification and phenotypic drug-susceptibility testing for mycobacteria are time-consuming and challenging but essential for managing mycobacterial infections. Next-generation sequencing (NGS) technologies can increase diagnostic speed and quality, but standardization is still lacking for many aspects (e.g., unbiased extraction, host depletion, bioinformatic analysis). Targeted PCR approaches directly on sample material are limited by the number of targets that can be included. Unbiased shotgun metagenomics on direct material is hampered by the massive amount of host DNA, which should be removed to improve the microbial detection sensitivity. For this reason, we developed a method for NGS-based diagnosis of mycobacteria directly from patient material. As a model, we used the non-tuberculous mycobacterium (NTM) Mycobacterium abscessus. We first compared the efficiency of three different DNA extraction kits for isolating DNA (quality and concentration). The two most efficient kits were then used in a follow-up study using artificial sputum. Finally, one extraction kit was selected and further evaluated for DNA isolation from a patients’ sputum mixture spiked with M. abscessus at three concentrations (final concentrations 108, 107, 106  CFU/ml). The spiked sputum samples were processed with and without saponin treatment (ST) in combination with DNAse treatment prior to bacterial DNA extraction to evaluate the recovery of bacteria and depletion of host DNA by PCR and Illumina sequencing.While Ct values of the qPCR targeting mycobacterial ITS DNA remained rather stable, Ct values in the qPCR targeting the human β-actin gene increased by five Ct values in ST samples. In subsequent Illumina sequencing, a decrease of 89% of reads mapped to the human genome was observed in ST samples. The percentage of reads mapped to M. abscessus (108 CFU/ml) increased by 89%, and the sequencing depth increased two times when undergoing ST.In conclusion, the sensitivity of M. abscessus detection in artificial sputum was increased using a saponin pre-treatment step. The saponin followed by the DNase I treatment approach could be efficiently applied to detect and characterize mycobacterial infections, including tuberculosis, directly from sputum.
Lesions causing post-stroke spasticity localize to a common brain network
Authors: Qin Yin , Qiu Shuting , Liu Xiaoying , Xu Shangwen , Wang Xiaoyang , Guo Xiaoping , Tang Yuting , Li Hui 
Published: October 2022

ObjectiveThe efficacy of clinical interventions for post-stroke spasticity (PSS) has been consistently unsatisfactory, probably because lesions causing PSS may occur at different locations in the brain, leaving the neuroanatomical substrates of spasticity unclear. Here, we investigated whether heterogeneous lesions causing PSS were localized to a common brain network and then identified the key nodes in this network.MethodsWe used 32 cases of PSS and the Human Connectome dataset (n = 1,000), using a lesion network mapping method to identify the brain regions that were associated with each lesion in patients with PSS. Functional connectivity maps of all lesions were overlaid to identify common connectivity. Furthermore, a split-half replication method was used to evaluate reproducibility. Then, the lesion network mapping results were compared with those of patients with post-stroke non-spastic motor dysfunction (n = 29) to assess the specificity. Next, both sensitive and specific regions associated with PSS were identified using conjunction analyses, and the correlation between these regions and PSS was further explored by correlation analysis.ResultsThe lesions in all patients with PSS were located in different cortical and subcortical locations. However, at least 93% of these lesions (29/32) had functional connectivity with the bilateral putamen and globus pallidus. These connections were highly repeatable and specific, as compared to those in non-spastic patients. In addition, the functional connectivity between lesions and bilateral putamen and globus pallidus in patients with PSS was positively correlated with the degree of spasticity.ConclusionWe identified that lesions causing PSS were localized to a common functional connectivity network defined by connectivity to the bilateral putamen and globus pallidus. This network may best cover the locations of lesions causing PSS. The putamen and globus pallidus may be potential key regions in PSS. Our findings complement previous neuroimaging studies on PSS, contributing to identifying patients with stroke at high risk for spasticity at an early stage, and may point to PSS-specific brain stimulation targets.
Nomogram to predict postoperative cognitive dysfunction in elderly patients undergoing gastrointestinal tumor resection
Authors: Huang Huifan , Chou Jing , Tang Yongzhong , Ouyang Wen , Wu Xiaoxia , Le Yuan 
Published: October 2022

ObjectiveTo establish a nomogram model for the prediction of postoperative cognitive dysfunction (POCD) in elderly patients undergoing gastrointestinal tumor resection.MethodsA total of 369 elderly patients scheduled for elective gastrointestinal tumor resection under general anesthesia were included. The cognitive function of each participant was assessed by the Mini-Mental State Examination (MMSE) 1 day before surgery and 7 days after surgery for the diagnosis of POCD. According to the results, patients were divided into a POCD group and a non-POCD group. The differences in hospitalization data and examination results between the two groups were compared. A logistic regression model was used to explore the risk factors for POCD in elderly patients undergoing gastrointestinal tumor resection, and a nomogram was then constructed based on these factors. The diagnostic performance of the nomogram was evaluated using the area under the receiver operating characteristic curve (AUROC) and a calibration plot. The clinical usefulness of the nomogram was estimated using decision curve analysis (DCA).ResultsAmong the 369 patients undergoing gastrointestinal tumor resection, 79 patients had POCD, with a positive rate of 21.4%. The nomogram model comprised the following variables: age, body mass index (BMI), history of cerebrovascular disease, preoperative white blood cell (WBC) count, preoperative hemoglobin (Hb) level, intra-operative blood loss, and operation time. The model showed good discrimination, with an area under the curve (AUC) of 0.710 (95% CI = 0.645–0.775), and good calibration (Hosmer–Lemeshow test, χ2 = 5.133, p = 0.274). Internal validation also maintained ideal discrimination and calibration. Decision curves indicated that when the threshold probability was above 0.1, the nomogram achieved more benefit than both the treat-all and treat-none policies.ConclusionThis scoring system is the first nomogram model developed for the prediction of POCD in elderly patients undergoing gastrointestinal tumor resection. It has good efficacy in the prediction of POCD risk and could provide an important reference for the prevention, management, and treatment of POCD.
Epidemiology, clinical presentation, treatment, and outcome of neurosarcoidosis: A mono-centric retrospective study and literature review
Authors: Sambon Pauline , Sellimi Amina , Kozyreff Alexandra , Gheysens Olivier , Pothen Lucie , Yildiz Halil , van Pesch Vincent 
Published: October 2022

IntroductionNeurosarcoidosis is a rare granulomatous disorder, and treatment guidelines are mainly based on retrospective studies.Materials and methodsThis retrospective study was performed to provide a detailed description of the clinical characteristics and treatment outcomes of patients with neurosarcoidosis followed at Cliniques Universitaires Saint Luc in Belgium. The second objective of our study was to perform a comparative literature review of neurosarcoidosis, with a focus on treatment outcomes with the use of TNF-α antagonist.ResultsAmong 180 patients with sarcoidosis followed in our hospital, 22 patients with neurosarcoidosis were included in the final analysis. Our literature research identified 776 articles of which 35 articles met our inclusion criteria, including 1,793 patients diagnosed with neurosarcoidosis. In our cohort, the majority of patients (86%) were diagnosed with systemic sarcoidosis which was similar to that reported in the literature (83%). Serum CRP and calcemia were elevated only in 33 and 18% of patients, respectively. Serum lysozyme and angiotensin-converting enzyme were elevated in 79 and 16% of patients, respectively. Lumbar puncture and CSF fluid analysis were performed in 15/22 patients and were abnormal in all patients. Brain MRI was performed in 21/22 patients and showed abnormalities in 16 patients consisting of parenchymal lesions in 63%, hypothalamic-pituitary axis lesions in 38%, and meningeal enhancement in 31%. In both cohort patients, methotrexate was the most frequently used treatment (&gt;45% of cases) with a favorable outcome in an average of 50% of patients. A TNF-α antagonist was administered in 9% of patients in our cohort and in 27% of patients in the literature review. The proportion of favorable outcomes in literature research was significantly higher in patients treated with TNF-α antagonists compared to methotrexate (p &lt; 0.0001), mycophenolate mofetil (p &lt; 0.0001), or azathioprine (p &lt; 0.0001).ConclusionThe results of our cohort and literature review confirm that neurosarcoidosis occurred most frequently in the context of systemic sarcoidosis. Methotrexate is the most frequent second-line therapy. The effectiveness of therapy with TNF-α antagonists is well-demonstrated and associated with a better outcome. Their earlier use during the disease course among aggressive and/or refractory neurosarcoidosis should be considered.
Use of reverse angle guide catheter with trans-radial approach in patients undergoing middle meningeal artery embolization
Authors: Krothapalli Neeharika , Fayad Mohamad , Patel Smit , Elmashad Ahmed , Sussman Eric , Bruno Charles , Grande Andrew , Jagadeesan Bharathi , Killory Brendan , Alberts Mark , Kureshi Inam , Ollenschleger Martin , Tummala Ramachandra , Mehta Tapan 
Published: October 2022

BackgroundTrans-radial access (TRA) for MMA embolization has grown due to lower access site complications and greater patient satisfaction. Here, we describe the feasibility of utilizing a 6F Envoy Simmons 2 (6F-SIM2) as a guide catheter with TRA and compare outcomes with trans-femoral approach (TFA) in a single center case series.MethodsWe performed a retrospective review of patients who underwent MMA embolization for management of chronic subdural hematoma (cSDH). TRA was performed by utilizing a combination of 6F 90cm Envoy (Codman &amp; Shurtleff, Inc., Rayham, MA) Simmons 2 guide catheter and 5F 125cm Sofia (Microvention, Aliso Viejo, CA) intermediate catheter. Outcomes measured are Modified Rankin Score (mRS) at 90 days, inpatient mortality, post-embolization recurrence, fluoroscopy time and radiation exposure.ResultsA total of 71 patients underwent 97 MMA embolization overall with 65 (67%) in trans-femoral access group, 11 (11.3%) in trans-radial access without use of Simmons 2 Guide catheter group and 21 (21.6%) in trans-radial access with use of Simmons 2 Guide catheter group. There were no direct access-related complications in either group. One patient had thromboembolic stroke in trans-femoral group. There was no difference in average procedure-related total fluro time or radiation dose among all three groups.ConclusionTrans-radial approach using 6F-SIM2 guide catheter coupled with 5F Sofia intermediate catheter is safe and effective. It provides an alternative approach to access distal branches of bilateral anterior circulation in elderly patients with difficult anatomy undergoing MMA embolization.
Association Between Dietary Fiber Intake and Risk of Depression in Patients With or Without Type 2 Diabetes
Authors: Mao Yafei , Li Xinyuan , Zhu Shumin , Geng Yulan 
Published: October 2022

BackgroundDepression and type 2 diabetes (T2D) are both serious public health problems, with morbidity and mortality in people increasing year by year, resulting in a heavy economic burden. A correlation between dietary fiber and both has been reported. Nevertheless, few data are available concerning dietary fiber and the risk of depression with or without T2D, which deserve further attention.Materials and MethodsWe assessed the relationship between dietary fiber intake and risk of depression with or without T2D in the 2007–2014 National Health and Nutrition Examination Survey (NHANES) population. A 24-h dietary review was used to assess fiber intake. The Patient Health Questionnaire-9 was used to assess depression. Stability of the results was assessed using restricted cubic spline models and logistic regression, as well as sensitivity analyses.ResultsA total of 17,866 adults aged 20 years and older with a mean age of 49.3 ± 17.7 years were included in this study, of whom 49.5% were male. After adjusting for covariates, the association of dietary fiber intake with the risk of depression appeared to differ between non-T2D group and T2D group (OR, 0.987; 95% CI, 0.979–0.995 vs. OR, 1.003; 95% CI, 0.988–1.017). Furthermore, when dietary fiber was converted to a categorical variable, there was evidence of interaction between T2D status and fiber intake on decreasing the prevalence of depression (P-value for interaction = 0.015). Sensitivity analysis showed stable results.ConclusionOur findings indicated that whether a patient has T2D may affect the relationship between dietary fiber intake and the risk of depression, which still needs to be confirmed by further randomized controlled trials.
Quantitative collateral score for the prediction of clinical outcomes in stroke patients: Better than visual grading
Authors: Lu Qingqing , Zhang Haiyan , Cao Xin , Fu Junyan , Pan Yuning , Zheng Xiaodong , Wang Jianhong , Geng Daoying , Zhang Jun 
Published: October 2022

ObjectivesTo identify preoperative prognostic factors for acute ischemic stroke (AIS) patients receiving mechanical thrombectomy (MT) and compare the performance of quantitative collateral score (qCS) and visual collateral score (vCS) in outcome prediction.MethodsFifty-five patients with AIS receiving MT were retrospectively enrolled. qCS was defined as the percentage of the volume of collaterals of both hemispheres. Based on the dichotomous outcome assessed using a 90-day modified Rankin Scale (mRS), we compared qCS, vCS, age, sex, National Institute of Health stroke scale score, etiological subtype, platelet count, international normalized ratio, glucose levels, and low-density lipoprotein cholesterol (LDL-C) levels between favorable and unfavorable outcome groups. Logistic regression analysis was performed to determine the effect on the clinical outcome. The discriminatory power of qCS, vCS, and their combination with cofounders for determining favorable outcomes was tested with the area under the receiver-operating characteristic curve (AUC).ResultsvCS, qCS, LDL-C, and age could all predict clinical outcomes. qCS is superior over vCS in predicting favorable outcomes with a relatively higher AUC value (qCS vs. vCS: 0.81 vs. 0.74) and a higher sensitivity rate (qCS vs. vCS: 72.7% vs. 40.9%). The prediction power of qCS + LDL-C + age was best with an AUC value of 0.91, but the accuracy was just increased slightly compared to that of qCS alone.ConclusionCollateral scores, LDL-C and age were independent prognostic predictors for patients with AIS receiving MT; qCS was a better predictor than vCS. Furthermore, qCS + LDL-C + age offers a strong prognostic prediction power and qCS alone was another good choice for predicting clinical outcome.