Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient climate simulations of the Holocene (version 1) – experimental design and boundary conditions

Abstract. The Holocene, which started approximately 11.5 ka, is the latest interglacial period with several rapid climate changes with timescales, from decades to centuries, superimposed on the millennium-scale mean climate trend. Climate models provide useful tools to investigate the underlying dynamic mechanisms for the climate change during this well-studied time period. Thanks to the improvements in the climate model and computational power, transient simulation of the Holocene offers an opportunity to investigate the climate evolution in response to time-varying external forcings and feedbacks. Here, we present the design of a new set of transient experiments for the whole Holocene from 11.5 ka to the preindustrial period (1850; HT-11.5 ka) to investigate both the combined and separated effects of the main external forcing of orbital insolation, atmospheric greenhouse gas (GHG) concentrations, and ice sheets on the climate evolution over the Holocene. The HT-11.5 ka simulations are performed with a relatively high-resolution version of the comprehensive Earth system model CESM1.2. 1 without acceleration, both fully and singly forced by time-varying boundary conditions of orbital configurations, atmospheric GHGs, and ice sheets. Preliminary simulation results show a slight decrease in the global annual mean surface air temperature from 11.5 to 7.5 ka due to both changes in orbital insolation and GHG concentrations, with an abrupt cooling at approximately 7.5 ka, which is followed by a continuous warming until the preindustrial period, mainly due to increased GHG concentrations. Both at global and zonal mean scales, the simulated annual and seasonal temperature changes at 6 ka lie within the range of the 14 PMIP4 model results and are overall stronger than their arithmetic mean results for the Middle Holocene simulations. Further analyses on the HT-11.5 ka transient simulation results will be covered by follow-up studies.
A More details of 3 D-CoreNet

The detailed architecture of our correspondence-refinement network (3D-CoreNet) is shown in Table 1. We take the vertices of the identity and pose meshes as inputs. Both of them are fed into the feature extractor and the adaptive feature block. The feature extractor consists of three Conv1dInstanceNorm-LeakyReLU blocks. Then we can calculate the optimal matching matrix with their features by solving an optimal transport problem. With the matrix, we warp the pose mesh to the coarse warped mesh. Finally, the warped mesh is better refined in the mesh refinement module with a set of elastic instance normalization residual blocks. The modulation parameters in the normalization layers are learned with elastic instance normalization.
Antibiotic susceptibility profile of bacteria isolated from fomites in some day care centres in Ile-Ife, Nigeria

This study was conducted by carrying out the isolation, identification and determination of the sensitivity profile to antibiotics in bacteria isolated from fomites in some day care centres in Ile-Ife, Osun State, Nigeria. A total of one hundred and twenty-four fomites were collected from selected seventeen day care centers within Ile-Ife. These were cultured on nutrient agar plates incubated at 37C for 24 h using streak plate technique. Preliminary identification of bacterial isolates was performed using cultural, colonial and morphological characteristics of isolates on the agar plates such as relative size, colour, texture, consistency, pigment, elevation, edge and shape. Bacterial isolates were further characterized by physiological characteristics through biochemical reactions of the bacterial isolates to some reagents and media with reference to the Bergey’s Manual of Determinative Bacteriology. Isolates were further identified with Microbact identification test kit. The antibiotype of the isolates was determined by the Kirby-Bauer’s disk diffusion technique. Detection of extended spectrum betalactamase was done phenotypically by the double disc synergy test. Resistance to antibiotics varied greatly among the isolates. Resistance to cefuroxime, augmentin, cephalexin and ampicillin was notably high in Bacillus sp, Staphylococcus sp, Corynebacterium sp and Staphylococcus aureus from fomites. Meanwhile, all Enterobacteriaceae were susceptible to meropenem, ciprofloxacin, augmentin, trimethroprim, gentamycin, cotrimoxazole, chloramphenicol and ofloxacin. Multiple antibiotic resistance (MAR) was generally high among the Gram positive isolates with diversity of MAR patterns.
Endovascular Thrombectomy in Young Patients With Stroke: A MR CLEAN Registry Study

Supplemental Digital Content is available in the text. Background and Purpose: Acute ischemic stroke due to large vessel occlusion is uncommon in young adults. We assessed stroke cause in young patients and compared their outcomes after endovascular thrombectomy with older patients. Methods: We used data (March 2014 until November 2017) of patients with an anterior circulation large vessel occlusion stroke from the MR CLEAN (Multicenter Randomized Controlled Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands) Registry, a nationwide, prospective study on endovascular thrombectomy in the Netherlands. We compared young patients (18–49 years) with older patients (≥50 years). Outcomes included modified Rankin Scale score after 90 days (both shift and dichotomized analyses), expanded Thrombolysis in Cerebral Infarction score, and symptomatic intracranial hemorrhage. Analyses were adjusted for confounding. Results: We included 3256 patients, 310 (10%) were 18 to 49 years old. Young patients had lower median National Institutes of Health Stroke Scale scores (14 versus 16, P<0.001) and less cardiovascular comorbidities than older patients. Stroke etiologies in young patients included carotid dissection (16%), cardio-embolism (15%), large artery atherosclerosis (10%), and embolic stroke of undetermined source (31%). Clinical outcome was better in young than older patients (acOR for modified Rankin Scale shift: 1.8 [95% CI, 1.5–2.2]; functional independence [modified Rankin Scale score 0–2] 61 versus 39% [adjusted odds ratio, 2.1 [95% CI, 1.6–2.8]); mortality 7% versus 32%, adjusted odds ratio, 0.2 [95% CI, 0.1–0.3]). Symptomatic intracranial hemorrhage occurred less frequently in young patients (3% versus 6%, adjusted odds ratio, 0.5 [95% CI, 0.2–1.00]). Successful reperfusion (expanded Thrombolysis in Cerebral Infarction Score 2b-3) did not differ between groups. Onset to reperfusion time was shorter in young patients (253 versus 255 minutes, adjusted B in minutes 12.4 [95% CI, 2.4–22.5]). Conclusions: Ten percent of patients with acute ischemic stroke undergoing endovascular thrombectomy were younger than 50. Cardioembolism and carotid dissection were common underlying causes in young patients. In one-third of cases, no cause was identified, indicating the need for more research on stroke cause in young patients. Young patients had better prognosis and lower risk of symptomatic intracranial hemorrhage than older patients.
The derivation of an International Classification of Diseases, Tenth Revision–based trauma-related mortality model using machine learning

Supplemental digital content is available in the text. BACKGROUND Existing mortality prediction models have attempted to quantify injury burden following trauma-related admissions with the most notable being the Injury Severity Score (ISS). Although easy to calculate, it requires additional administrative coding. International Classification of Diseases (ICD)–based models such as the Trauma Mortality Prediction Model (TMPM-ICD10) circumvent these limitations, but they use linear modeling, which may not adequately capture the intricate relationships of injuries on mortality. Using ICD-10 coding and machine learning (ML) algorithms, the present study used the National Trauma Data Bank to develop mortality prediction models whose performance was compared with logistic regression, ISS, and TMPM-ICD10. METHODS The 2015 to 2017 National Trauma Data Bank was used to identify adults following trauma-related admissions. Of 8,021 ICD-10 codes, injuries were categorized into 1,495 unique variables. The primary outcome was in-hospital mortality. eXtreme Gradient Boosting (XGBoost), a ML technique that uses iterations of decision trees, was used to develop mortality models. Model discrimination was compared with logistic regression, ISS, and TMPM-ICD10 using receiver operating characteristic curve and probabilistic accuracy with calibration curves. RESULTS Of 1,611,063 patients, 54,870 (3.41%) experienced in-hospital mortality. Compared with those who survived, those who died more frequently suffered from penetrating trauma and had a greater number of injuries. The XGBoost model exhibited superior receiver operating characteristic curve (0.863 [95% confidence interval (CI), 0.862–0.864]) compared with logistic regression (0.845 [95% CI, 0.844–0.846]), ISS (0.828 [95% CI, 0.827–0.829]), and TMPM-ICD10 (0.861 [95% CI, 0.860–0.862]) (all p < 0.001). Importantly, the ML model also had significantly improved calibration compared with other methodologies (XGBoost, coefficient of determination (R2) = 0.993; logistic regression, R2 = 0.981; ISS, R2 = 0.649; TMPM-ICD10, R2 = 0.830). CONCLUSION Machine learning models using XGBoost demonstrated superior performance and calibration compared with logistic regression, ISS, and TMPM-ICD10. Such approaches in quantifying injury severity may improve its utility in mortality prognostication, quality improvement, and trauma research. LEVEL OF EVIDENCE Prognostic and Epidemiologic; level III.
Inhibition of the Interaction of TREM-1 and eCIRP Attenuates Inflammation and Improves Survival in Hepatic Ischemia/Reperfusion

ABSTRACT Introduction: Triggering receptor expressed on myeloid cells-1 (TREM-1) has important implications in sepsis and inflammation and is a novel receptor for extracellular cold-inducible RNA-binding protein (eCIRP). We hypothesize that the inhibition of TREM-1 via its interaction with eCIRP by novel peptide inhibitor M3 or knockout gene will attenuate the inflammation and injury associated with severe hepatic ischemia/reperfusion (I/R). Methods: Wild-type (WT) C57BL/6 and TREM-1-/- mice underwent 60 min of 70% hepatic ischemia, with 24 h of reperfusion. Additionally, WT mice underwent hepatic I/R and were treated with M3 (10 mg/kg body weight) or vehicle (normal saline) at the start of reperfusion. Blood and ischemic liver tissues were collected, and analysis was performed using enzymatic assays, enzyme-linked immunosorbent assay, reverse-transcription quantitative polymerase chain reaction, and pathohistology techniques. For survival surgery, mice additionally underwent resection of non-ischemic lobes of the liver and survival was monitored for 10 days. Results: There was an increase in serum levels of tissue markers including aspartate aminotransferase, alanine aminotransferase, and lactate dehydrogenase as well as cytokine levels (IL-6) and histological scoring of hematoxylin and eosin sections in WT I/R mice. These markers decreased substantially in TREM-1-/- mice. Additionally, neutrophil infiltration markers and markers of local inflammation (myeloperoxidase, macrophage inflammatory protein-2, cyclooxygenase-2) were attenuated in TREM-1-/- mice. Similarly, we show a significant decrease in injury and inflammation markers with M3 treatment. Additionally, we demonstrate decreased apoptosis with TREM-1 inhibition. Finally, M3 treatment improved the survival rate from 42% to 75% after hepatic I/R. Conclusion: TREM-1 is an important eCIRP receptor in the inflammatory response of hepatic I/R, and deficiency of TREM-1 via knockout gene or peptide inhibition attenuated liver injury and inflammation, and improved survival. Inhibition of the TREM-1 and eCIRP interaction in hepatic I/R may have important therapeutic potential.
Ranibizumab and conbercept for treating wet age-related macular degeneration in China

Abstract Background: This study aimed to evaluate the therapeutic effects of ranibizumab and conbercept on wet age-related macular degeneration. Methods: Randomized controlled trials comparing ranibizumab and conbercept in the treatment of wet age-related macular degeneration were searched in the PubMed, Medline, EMbase, Cochrane Library, China National Knowledge Infrastructure, Wanfang databases, and Weipu Journal. Two reviewers independently extracted the data and assessed the methodological quality. Data analysis was performed using Rev Man 5.3 software for statistical analysis. Results: A total of 16 randomized controlled trials, including 1018 patients, were included, and the results showed that the effect of ranibizumab on uncorrected visual acuity was not significantly different from that of conbercept (Mean difference [MD] = -.03, 95% Confidence interval [CI] [-.10-.05], P = .47), and there was no significant difference between the two drugs in the effect on best-corrected visual acuity (MD = .00, 95% CI [-.02-.03], P = .73). The effect of conbercept on intraocular pressure was better than that of ranibizumab (MD = 1.61, 95% CI [1.05-2.17], P < .001). The effect of ranibizumab on central macular thickness was not significantly different from that of conbercept (MD = 1.31, 95% CI [-3.81-6.43], P = .62). Conbercept had a better inhibitory effect on choroidal neovascularization than ranibizumab (MD = .49, 95% CI [.32-.76], P = .001). Conclusion: The effects of ranibizumab on uncorrected visual acuity, best corrected visual acuity, and central macular thickness were not significantly different from those of conbercept. Conbercept is associated with a lower risk of increased intraocular pressure and regression of choroidal neovascularization compared with ranibizumab.
Resection of esophageal duplication cyst in a 6-month child: a surgical challenge by video-assisted thoracoscopic surgery VATS

Introduction and importance: Esophageal duplication cysts (EDCs) are rare congenital entities, with an incidence of 1:100,00. The majority of patients are asymptomatic and lesions are usually found incidentally on imaging. However, these cysts were removed via open surgery. Nowadays, video-assisted thoracoscopy surgery (VATS) is an alternative safe method to remove ECDs. Case presentation: Here we present a 6-month-child male complaining of shortness of breath, stridor associated with cough, repeated vomiting, and fever. Furthermore, laboratory test results are within normal limits. Chest x-ray showed well-defined soft tissue density on the right upper and middle lobe with normal lung field, and computed tomography scan revealed that cystic lesion measuring 7×3 cm extended from the thyroid cartilage downward to the posterior mediastinum and toward the right side of the chest causing compression of the trachea, esophagus, and right mainstem bronchus. Finally, the patient was diagnosed with an EDC by histopathologic examination. The patient underwent surgery under general anesthesia by uni-portal VATS through the right fourth intercostal space was performed. The cyst was resected, and an esophageal tear occurred because of the wall of the esophagus as part of the cyst. The patient was discharged on day 11 postoperative. Conclusion: EDC is an exceedingly rare entity. VATS is a less invasive procedure, effective, safe, and has a good clinical outcome compared with open surgical resection. We conclude that EDC should be maintained in the differential diagnosis of unexplained stridor, wheeze, and recurrent chest infection in children.
End-tidal Carbon Dioxide for Diagnosing Anaphylaxis in Patients with Severe Postinduction Hypotension

Background: Perioperative hypersensitivity reactions may be difficult to diagnose during general anesthesia. Postinduction hypotension is the most common sign but is not specific. It was recently suggested that low end-tidal carbon dioxide (ETco2) might be a marker of anaphylaxis (Ring and Messmer grades III to IV immediate hypersensitivity reactions) in hypotensive patients under mechanical ventilation. To test this hypothesis, the authors compared ETco2 in patients with a diagnosis of anaphylaxis and in patients with severe hypotension from any other cause after the induction of anesthesia. Methods: This was a retrospective single-center case-control study in which two groups were formed from an anesthesia data warehouse. The anaphylaxis group was formed on the basis of tryptase/histamine assay data and allergy workup data recorded over the period 2010 to 2018. The control (hypotension) group consisted of all patients having experienced severe hypotension (mean arterial pressure less than 50 mmHg for 5 min or longer) with a cause other than anaphylaxis after anesthesia induction in 2017. Results: The anaphylaxis and hypotension groups comprised 49 patients (grade III: n = 38; grade IV: n = 11) and 555 patients, respectively. The minimum ETco2 value was significantly lower in the anaphylaxis group (median [interquartile range]: 17 [12 to 23] mmHg) than in the hypotension group (32 [29 to 34] mmHg; P < 0.001). The area under the receiver operating characteristic curve (95% CI) for ETco2 was 0.95 (0.91 to 0.99). The sensitivity and specificity (95% CI) for the optimal cutoff value were 0.92 (0.82 to 0.98) and 0.94 (0.92 to 0.99), respectively. In multivariable analysis, minimum ETco2 was associated with anaphylaxis after adjusting for confounders and competing predictors, including arterial pressure, heart rate, and peak airway pressure (odds ratio [95% CI] for ETco2: 0.51 [0.38 to 0.68]; P < 0.001). Conclusions: In case of severe hypotension after anesthesia induction, a low ETco2 contributes to the diagnosis of anaphylaxis, in addition to the classical signs of perioperative immediate hypersensitivity. From a retrospective single-center case-control study comparing low end-tidal carbon dioxide (ETco2) postinduction in hypotensive patients due to anaphylaxis compared to other causes, a low ETco2 contributed to the diagnosis of anaphylaxis. The results therefore suggest that in mechanically ventilated patients with severe postinduction hypotension, ETco2 should be considered as one of the means of distinguishing between anaphylaxis and other potential causes.
Variable neurological phenotypes of homocystinuria caused by biallelic methylenetetrahydrofolate reductase variants

Inherited methylenetetrahydrofolate reductase (MTHFR) deficiency is associated with a wide spectrum of disorders including homocystinuria. This study aims to describe the neurological phenotypes and molecular profiles of patients with homocystinuria caused by biallelic variants in MTHFR. We report six subjects with MTHFR deficiency who presented with variable neurological phenotypes which could be viewed as a continuous spectrum. Fatal infantile encephalopathy was observed in one family, whereas another patient presented at 27 years with acute leukoencephalopathy and recovered within 3 months. Intermediate forms presenting as complicated hereditary spastic paraparesis of variable severity were observed in four subjects. Clinical and molecular information of the 207 cases reported in literature were also retrieved and analyzed. We categorized all subjects into three categories - severe, intermediate and mild forms according to the clinical presentation. In addition, a total of 286 disease-causing variations reported to date were analyzed. These included seven disease-causing variants reported in this study of which one is novel. Some genotype-phenotype correlation could be seen which corroborated with previous observations. However, inter- and intrafamilial variability was also noted. Treatment with betaine, B12 and folic acid was started in four subjects with variable outcomes.
The effect of prone position for ventilator-associated pneumonia in adult patients: a systematic review and meta-analysis

Supplemental Digital Content is available in the text Abstract Background: The effect and safety of prone position (PP) in ventilator-associated pneumonia (VAP) patients was uncertain. We systematically reviewed the literature published to investigate whether PP benefits for patients with VAP compared with conventional supine position (SP). Methods: PubMed, EMbase, Cochrane Library, CNKI and WanFang Database were electronically searched to collect randomized controlled trials (RCTs) about the PP ventilation and SP ventilation in intensive care unit (ICU) patients from inception to May 2020. Meta-analysis was performed by Revan 5.3 software. Results: A total of 7 RCTs involving 1604 patients were included. Compared to regular SP ventilation, the PP ventilation group had no statistical significance in the four aspects. The results of subgroup analysis showed that the incidence of VAP and all-cause mortality were not affected by the patient's initial oxygenation index. However, the incidence of VAP tended to decrease when the duration of PP ventilation was less than 16 hours per day. Meanwhile, the all-cause mortality was significantly decreased while the daily time was more than 16 hours. Conclusions: Current evidence showed that the PP ventilation could not decrease the incidence of VAP, all-cause mortality, length of mechanical ventilation, and ICU stay. However, the daily duration of PP ventilation may have an impact on the incidence of VAP and all-cause mortality in critical patients.
Bile acids, bile pigments and colorectal cancer risk

Purpose of review The gut microbial co-metabolism of bile-derived compounds (e.g. bile acids and bile pigments) affects colorectal cancer (CRC) risk. Here, we review recent findings with focus on selected novel aspects of bile-associated effects with interesting but unclear implications on CRC risk. Recent findings Numerous studies demonstrated novel biotransformation of bile acids by gut bacteria (e.g. microbial conjugation of bile acids), resulting in diverse bile acid compounds that show complex interactions with host receptors (e.g. FXR, TGR5). In addition, YAP-associated signalling in intestinal epithelial cells is modulated via bile acid receptor TGR5 and contributes to colonic tumorigenesis. Finally, studies indicate that serum levels of the bile pigment bilirubin are inversely associated with CRC risk or intestinal inflammation and that bilirubin affects gut microbiota composition. Summary Bile acids and bile pigments have multiple effects on intestinal microbe-host interactions, which may collectively modulate long-term CRC risk of the host.