bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of systemic lupus erythematosus on the 5-year survival of critically ill septic patients
Authors: Chen Hsin-Hua , Chen Hsian-Min , Chen Yi-Ming , Chen Yi-Hsing , Lin Ching-Heng , Chao Wen-Cheng 
Published: October 2021

Abstract
Background
Infectious disease is an increasing threat to patients with systemic lupus erythematosus (SLE); however, the long-term outcome in critically ill septic patients with SLE remains unclear, and we aimed to address the impact of SLE on 5-year survival in critically ill septic patients.

Methods
We used the 2003–2017 nationwide data with 825,556 patients with sepsis in Taiwan. We identified lupus cases with sepsis that required admission to the intensive care unit and mechanical ventilation and selected controls matched (1:4) for age, sex, and index-year. Conditional logistic regression analysis was used to determine risk factors for mortality risk and shown as odds ratios (HRs) with 95% confidence intervals (CIs).

Results
A total of 513 SLE-sepsis patients and 2052 matched non-SLE septic individuals were enrolled. The mortality rate was higher in the SLE group (38.5 per 100,000 person-year) than that in the non-SLE group (13.7 per 100,000 person-year), with an IRR of 2.8 (95% CI, 2.5–3.2). We found that SLE was independently associated with a high mortality rate after adjusting relevant variables (HR 1.47, 95% CI 1.27–1.77). In addition to SLE, a higher age (HR 1.02, 95% CI 1.02–1.02), more comorbidities, and receiving prednisolone equivalent dose higher than 5 mg/day (HR 1.55, 95% CI 1.27–1.90), methotrexate (HR 2.19, 95% CI 1.61–2.99), and immunosuppressants (HR 1.45, 95% CI 1.22–1.74) were also independent risks for mortality.

Conclusions
We identified that SLE affects the long-term mortality in critically ill septic patients, and more studies are warranted for the underlying mechanism.
Noninvasive assessment of kidney dysfunction in children by using blood oxygenation level-dependent MRI and intravoxel incoherent motion diffusion-weighted imaging
Authors: Liang Ping , Chen Yaxian , Li ShiChao , Xu Chuou , Yuan Guanjie , Hu Daoyu , Kamel Ihab , Zhang Yu , Li Zhen 
Published: October 2021

Abstract
Objectives
To explore whether multiparametric approach including blood oxygenation level-dependent MRI (BOLD-MRI) and intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) can be applied in the assessment of renal function in children with chronic kidney disease (CKD).

Materials and methods
This prospective study included 74 children (CKD stage 1–3, 51; CKD stage 4–5, 12; healthy volunteers, 11) for renal MRI examinations including coronal T2WI, axial T1WI and T2WI, BOLD-MRI, and DWI sequences. We measured the renal cortex and medulla T2*, ADC, Dt, Dp, and fp values on BOLD and DWI images. Appropriate statistical methods were applied for comparing MRI-derived parameters among the three groups and calculating the correlation coefficients between MRI-derived parameters and clinical data. Receiver operating characteristic (ROC) curves were used to assess the diagnostic performance of MRI-derived parameters.

Results
There were significant differences in cortex T2*, ADC, Dt, fp and medulla T2*, ADC, Dt among the three groups. Cortex T2*, ADC, Dt, fp and medulla T2*, ADC, Dt had a trend: CKD stage 4–5 < CKD stage 1–3 < healthy volunteers. Cortex and medulla T2*, ADC, Dt were significantly correlated with eGFR, serum creatinine (Scr), cystatin C. In addition, cortex T2* and eGFR showed the highest correlation coefficient (r = 0.824, p < 0.001). Cortex Dt and medulla T2* were optimal parameters for differentiating healthy volunteers and CKD stage 1–3 or CKD stage 4–5 and CKD stage 1–3, respectively.

Conclusions
BOLD-MRI and IVIM-DWI might be used as a feasible method for noninvasive assessment of renal function in children with CKD.
The brainstem in multiple sclerosis: MR identification of tracts and nuclei damage
Authors: Nguyen Thien Huong , Vaussy Alexis , Le Gaudu Violette , Aboab Jennifer , Espinoza Sophie , Curajos Irina , Heron Emmanuel , Habas Christophe 
Published: October 2021

Abstract
Objective
To evaluate the 3D Fast Gray Acquisition T1 Inversion Recovery (FGATIR) sequence for MRI identification of brainstem tracts and nuclei damage in multiple sclerosis (MS) patients.

Methods
From april to december 2020, 10 healthy volunteers and 50 patients with remitted-relapsing MS (58% female, mean age 36) underwent MR imaging in the Neuro-imaging department of the C.H.N.O. des Quinze-Vingts, Paris, France. MRI was achieved on a 3 T system (MAGNETOM Skyra) using a 64-channel coil. 3D FGATIR sequence was first performed on healthy volunteers to classify macroscopically identifiable brainstem structures. Then, FGATIR was assessed in MS patients to locate brainstem lesions detected with Proton Density/T2w (PD/T2w) sequence.

Results
In healthy volunteers, FGATIR allowed a precise visualization of tracts and nuclei according to their myelin density. Including FGATIR in MR follow-up of MS patients helped to identify structures frequently involved in the inflammatory process. Most damaged tracts were the superior cerebellar peduncle and the transverse fibers of the pons. Most frequently affected nuclei were the vestibular nuclei, the trigeminal tract, the facial nerve and the solitary tract.

Conclusion
Combination of FGATIR and PD/T2w sequences opened prospects to define MS elective injury in brainstem tracts and nuclei, with particular lesion features suggesting variations of the inflammatory process within brainstem structures. In a further study, hypersignal quantification and microstructure information should be evaluated using relaxometry and diffusion tractography. Technical improvements would bring novel parameters to train an artificial neural network for accurate automated labeling of MS lesions within the brainstem.
Red blood cells and their releasates compromise bone marrow-derived human mesenchymal stem/stromal cell survival in vitro
Authors: Dregalla Ryan Christopher , Herrera Jessica Ann , Donner Edward Jeffery 
Published: October 2021

Abstract
Purpose
The use of bone marrow aspirate (BMA) and bone marrow aspirate concentrate (BMC) in the treatment of inflammatory orthopedic conditions has become a common practice. The therapeutic effect of BMA/BMC is thought to revolve primarily around the mesenchymal stem/stromal cell (MSC) population residing within the nucleated cell fraction. MSCs have the unique ability to respond to site of injury via the secretion of immunomodulating factors, resolving inflammation in diseased joints. Recently, the importance of hematocrit (HCT) in BMC has been debated, as the potential impact on MSC function is unknown. In the present study, we investigate MSC health over a short time-course following exposure to a range of HCT and red blood cell releasate (RBCrel) conditions.

Methods
Bone marrow-derived human MSCs in early passage were grown under conditions of 0%, 2.5%, 5%, 10%, 20% and 40% HCT and RBCrel conditions for 3 days. At each day, the percentage of viable, apoptotic and necrotic MSCs was determined via flow cytometry. Relative viable MSC counts in each condition was determined to account for dynamic changes in overall MSC densities over the time-course. Statistical analysis was performed using a one-way ANOVA comparing test conditions to the control followed by a Dunnett’s multiple comparison test.

Results
Significant reductions in viable MSCs concurrent with an increase in necrotic MSCs in high HCT and RBCrel conditions was observed within 24 h. At each successive timepoint, the percent and relative number of viable MSCs were reduced, becoming significant in multiple HCT and RBCrel conditions by Day 3. Necrosis appears to be the initial mode of MSC death following exposure to HCT and RBCrel, followed by apoptosis in surviving MSC fractions.

Conclusion
Various levels of HCT and RBCrel severely compromise MSC health within 3 days and HCT should be controlled in the preparation of BMC products. Further, HCT of BMCs should be routinely recorded and tracked with patient outcomes along with routine metrics (e.g. nucleated cell counts, fibroblast-colony forming units). Differences in HCT may account for the inconsistencies in the efficacy of BMC reported when treating orthopedic conditions.
Induced pluripotent stem cells can improve thrombolytic effect of low-dose rt-PA after acute carotid thrombosis in rat
Authors: Hsieh Hsi-Lung , Liang Ching-Chung , Lu Cheng-You , Yang Jen-Tsung , Chung Chiu-Yen , Ko Yu-Shien , Lee Tsong-Hai 
Published: October 2021

Abstract
Background
Intravenous thrombolysis using recombinant tissue plasminogen activator (rt-PA) is the standard treatment for acute ischemic stroke. Standard-dose rt-PA (0.9 mg/kg) is known to achieve good recanalization but carries a high bleeding risk. Lower dose of rt-PA has less bleeding risk but carries a high re-occlusion rate. We investigate if induced pluripotent stem cells (iPSCs) can improve the thrombolytic effect of low-dose rt-PA (0.45 mg/kg).

Methods
Single irradiation with 6 mW/cm2 light-emitting diode (LED) for 4 h at rat common carotid artery was used as thrombosis model according to our previous report. Endothelin-1 (ET-1), intercellular adhesion molecule-1 (ICAM-1), and interleukin 1 beta (IL-1 beta) were used as the inflammatory markers for artery endothelial injury. Angiopoietin-2 (AP-2), brain-derived neurotrophic factor (BDNF) and vascular endothelial growth factor (VEGF) were examined in artery wall and iPSCs culture. Animal ultrasound was used to evaluate the stenosis degree of common carotid artery before and at 2 h, 24 h, 4 days and 7 days after LED irradiation.

Results
After LED irradiation alone, there was a persistent occlusion from 2 h to 7 days. Standard-dose rt-PA alone could recanalize the occluded artery from 24 h to 7 days to stenotic degree ≤ 50%. Low-dose rt-PA or 1 × 106 mouse iPSCs alone could not recanalize the occluded arteries from 2 h to 7 days. Combination use of low-dose rt-PA plus 1 × 106 mouse iPSCs caused better recanalization from 24 h to 7 days. ET-1, ICAM-1 and IL-1 beta were strongly expressed after LED irradiation but reduced after iPSCs treatment. AP-2, BDNF and VEGF were rarely induced after LED irradiation but strongly expressed after iPSCs treatment. In vitro study showed iPSCs could express AP-2, BDNF and VEGF.

Conclusion
The adjuvant use of iPSCs may help improving the thrombolytic effect of low-dose rt-PA by suppressing inflammatory factors and inducing angiogenic trophic factors. Stem cells could be a potential regimen in acute thrombolytic therapy to improve recanalization and reduce complications.
Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises
Authors: Sandholt Arnar K. S. , Neimanis Aleksija , Roos Anna , Eriksson Jenny , Söderlund Robert 
Published: October 2021

AbstractA type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (“Fulica-like”) has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections.
Head-mounted accelerometry accurately detects prey capture in California sea lions
Authors: Cole Mason R. , Zeligs Jenifer A. , Skrovan Stefani , McDonald Birgitte I. 
Published: October 2021

AbstractDetecting when and where animals feed is key to understanding their ecophysiology, but our ability to collect these data in marine mammals remains limited. Here, we test a tag-based accelerometry method to detect prey capture in California sea lions. From synchronized underwater video and acceleration data of two trained sea lions, we isolated a combined acceleration and Jerk pattern that reliably indicated prey capture in training datasets. We observed a stereotyped feeding motion in underwater video that included (1) mouth opening while approaching prey; (2) head deceleration to allow initial suction or prey engulfment, and (3) jaw closure. This motion (1–3) was repeated if a prey item was not initially engulfed. This stereotyped feeding motion informed a signal pattern phrase that accurately detected feeding in a training dataset. This phrase required (1) an initial heave-axis Jerk signal surpassing a threshold based on sampling rate; (2) an estimated dynamic surge-axis deceleration signal surpassing −0.7 g beginning within 0.2 s of the initial Jerk signal; and (3) an estimated dynamic surge-axis acceleration signal surpassing 1.0 g within 0.5 s of the beginning of the prior deceleration signal. We built an automated detector in MATLAB to identify and quantify these patterns. Blind tests of this detector on non-training datasets found high true-positive detection rates (91%–100%) with acceleration sampled at 50–333 Hz and low false-positive detection rates (0%–4.8%) at all sampling rates (16–333 Hz). At 32 Hz and below, true-positive detection rates decreased due to attenuation of signal detail. A detector optimized for an adult female was also accurate at 32–100 Hz when tested on an adult male’s data, suggesting the potential future use of a generalized detector in wild subjects. When tested on the same data, a published triaxial Jerk method produced high true-positive detection rates (91–100%) and low-to-moderate false-positive detection rates (15–43%) at ≥ 32 Hz. Using our detector, larger prey elicited longer prey capture duration in both animals at almost all sampling rates 32 Hz or faster. We conclude that this method can accurately detect feeding and estimate relative prey length in California sea lions.
Days to visit an offshore island: effect of weather conditions on arrival fuel load and potential flight range for common blackbirds Turdus merula migrating over the North Sea
Authors: Kelsey Natalie A. , Hüppop Ommo , Bairlein Franz 
Published: October 2021

AbstractBackgroundCrossing open water instead of following the coast(line) is one way for landbirds to continue migration. However, depending on prevailing weather and the birds’ physiological conditions, it is also a risky choice. To date, the question remains as to which interplay between environmental and physiological conditions force landbirds to stop on remote islands. We hypothesise that unfavourable winds affect lean birds with low energy resources, while poor visibility affects all birds regardless of their fuel loads.MethodsTo test this hypothesis, we caught 1312 common blackbirdsTurdus merulastopping over on Helgoland during autumn and spring migration. Arrival fuel load was measured using quantitative magnetic resonance technology. Weather parameters (wind and relative humidity as a proxy for visibility) were interpolated for the night before arrival. Further, we calculated whether caught individuals would have successfully crossed the North Sea instead of landing on Helgoland, depending on wind conditions.ResultsBoth wind and relative humidity the night before arrival were correlated with arrival fuel load. After nights with strong headwinds, birds caught the following day were mostly lean, most of which would not have managed to cross the sea if they had not stopped on Helgoland. In contrast, fat birds that could have successfully travelled on were caught mainly after nights with high relative humidity (≥ 80%). Furthermore, the rate of presumably successful flights was lower due to wind: although only 9% of all blackbirds captured on Helgoland had insufficient fuel loads to allow safe onward migration in still air, real wind conditions would have prevented 30% of birds from successfully crossing the sea during autumn and 21% during spring migration.ConclusionsWe were able to decipher how physiological condition, wind and relative humidity partially force blackbirds to stop on a remote island. Adverse winds tend to affect lean birds with low energy resources, while poor visibility can affect blackbirds, regardless of whether the arrival fuel load was sufficient for onward flight. Our findings will help to understand different migratory strategies and explain further questions like migration timing.
Deep learning reveals disease-specific signatures of white matter pathology in tauopathies
Authors: Vega Anthony R. , Chkheidze Rati , Jarmale Vipul , Shang Ping , Foong Chan , Diamond Marc I. , White Charles L. , Rajaram Satwik 
Published: October 2021

AbstractAlthough pathology of tauopathies is characterized by abnormal tau protein aggregation in both gray and white matter regions of the brain, neuropathological investigations have generally focused on abnormalities in the cerebral cortex because the canonical aggregates that form the diagnostic criteria for these disorders predominate there. This corticocentric focus tends to deemphasize the relevance of the more complex white matter pathologies, which remain less well characterized and understood. We took a data-driven machine-learning approach to identify novel disease-specific morphologic signatures of white matter aggregates in three tauopathies: Alzheimer disease (AD), progressive supranuclear palsy (PSP), and corticobasal degeneration (CBD). We developed automated approaches using whole slide images of tau immunostained sections from 49 human autopsy brains (16 AD,13 CBD, 20 PSP) to identify cortex/white matter regions and individual tau aggregates, and compared tau-aggregate morphology across these diseases. Tau burden in the gray and white matter for individual subjects strongly correlated in a highly disease-specific fashion. We discovered previously unrecognized tau morphologies for AD, CBD and PSP that may be of importance in disease classification. Intriguingly, our models classified diseases equally well based on either white or gray matter tau staining. Our results suggest that tau pathology in white matter is informative, disease-specific, and linked to gray matter pathology. Machine learning has the potential to reveal latent information in histologic images that may represent previously unrecognized patterns of neuropathology, and additional studies of tau pathology in white matter could improve diagnostic accuracy.
Trench and drilling investigation of the Median Tectonic Line in Shikoku, southwest Japan: implications for fault geometry
Authors: Miyawaki Masahiro , Sakaguchi Arito 
Published: October 2021

AbstractThe Median Tectonic Line (MTL) is a thousand-kilometer-long fault that extends across southwest Japan. Near the Nyugawa region of Shikoku, the MTL comprises (i) a low-angle inactive terrane boundary fault (the MTLTB) that divides the Jurassic and Cretaceous geological terranes, and (ii) a subparallel high-angle active fault zone (the MTLAFZ; Kawakami Fault). To better understand the relationship between the MTLTB and MTLAFZ fault traces, we exposed a ten-meter-long trench of approximately 2-m depth across the Kawakami Fault. We also drilled and cored five boreholes with lengths 80‒330 m along a 100 m transect to understand the cross-cutting relationship between the MTL faults and to determine the fault plane geometries and their dipping values. The Kawakami Fault was found to be a high-angle (> 70°) active fault exposed at the surface; however, it represents a non-vertical or listric fault that converges to the low-angle MTLTB fault dipping to the north at 30°. The Kawakami Fault was originally formed as a reverse fault, and subsequent dextral strike–slip displacement occurred along the same fault plane. Although the MTLTB is poorly oriented with respect to the regional stress field, it is capable of rupturing owing to its significantly weak interface; the properties of local faulted rock material are expected to play an important role in determining slip behavior.
Quantitative analysis on photon numbers received per cell for triggering β-carotene accumulation in Dunaliella salina
Authors: Xi Yimei , Xue Song , Cao Xupeng , Chi Zhanyou , Wang Jinghan 
Published: October 2021

Abstract
Accumulation of β-carotene in Dunaliella salina is highly dependent on light exposure intensity and duration, but quantitative analysis on photon numbers received per cell for triggering β-carotene accumulation is not available so far. In this study, experiment results showed that significant β-carotene accumulation occurred after at least 8 h illumination at 400 µmol photons·m−2·s−1. To quantify the average number of photons received per cell, correlations of light attenuation with light path, biomass concentration, and β-carotene content were, respectively, established using both Lambert–Beer and Cornet models, and the latter provided better simulation. Using Cornet model, average number of photons received per cell (APRPC) was calculated and proposed as a parameter for β-carotene accumulation, and constant APRPC was maintained by adjusting average irradiance based on cell concentration and carotenoids content changes during the whole induction period. It was found that once APRPC reached 0.7 µmol photons cell−1, β-carotene accumulation was triggered, and it was saturated at 9.9 µmol photons cell−1. This study showed that APRPC can be used as an important parameter to precisely simulate and control β-carotene production by D. salina.

Graphic Abstract