bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modular framework for the development of targeted Covid-19 blood transcript profiling panels
Authors: Rinchai Darawan , Syed Ahamed Kabeer Basirudeen , Toufiq Mohammed , Tatari-Calderone Zohreh , Deola Sara , Brummaier Tobias , Garand Mathieu , Branco Ricardo , Baldwin Nicole , Alfaki Mohamed , Altman Matthew C. , Ballestrero Alberto , Bassetti Matteo , Zoppoli Gabriele , De Maria Andrea , Tang Benjamin , Bedognetti Davide , Chaussabel Damien 
Published: July 2020

Abstract
Background
Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of targeted blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection.

Methods
We designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates.

Results
As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: immunological relevance, therapeutic development relevance and SARS biology relevance.

Conclusion
Altogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients.
Meta-analysis of mouse transcriptomic studies supports a context-dependent astrocyte reaction in acute CNS injury versus neurodegeneration
Authors: Das Sudeshna , Li Zhaozhi , Noori Ayush , Hyman Bradley T. , Serrano-Pozo Alberto 
Published: July 2020

Abstract
Background
Neuronal damage in acute CNS injuries and chronic neurodegenerative diseases is invariably accompanied by an astrocyte reaction in both mice and humans. However, whether and how the nature of the CNS insult—acute versus chronic—influences the astrocyte response, and whether astrocyte transcriptomic changes in these mouse models faithfully recapitulate the astrocyte reaction in human diseases remains to be elucidated. We hypothesized that astrocytes set off different transcriptomic programs in response to acute versus chronic insults, besides a shared “pan-injury” signature common to both types of conditions, and investigated the presence of these mouse astrocyte signatures in transcriptomic studies from human neurodegenerative diseases.

Methods
We performed a meta-analysis of 15 published astrocyte transcriptomic datasets from mouse models of acute injury (n = 6) and chronic neurodegeneration (n = 9) and identified pan-injury, acute, and chronic signatures, with both upregulated (UP) and downregulated (DOWN) genes. Next, we investigated these signatures in 7 transcriptomic datasets from various human neurodegenerative diseases.

Results
In mouse models, the number of UP/DOWN genes per signature was 64/21 for pan-injury and 109/79 for acute injury, whereas only 13/27 for chronic neurodegeneration. The pan-injury-UP signature was represented by the classic cytoskeletal hallmarks of astrocyte reaction (Gfap and Vim), plus extracellular matrix (i.e., Cd44, Lgals1, Lgals3, Timp1), and immune response (i.e., C3, Serping1, Fas, Stat1, Stat2, Stat3). The acute injury-UP signature was enriched in protein synthesis and degradation (both ubiquitin-proteasome and autophagy systems), intracellular trafficking, and anti-oxidant defense genes, whereas the acute injury-DOWN signature included genes that regulate chromatin structure and transcriptional activity, many of which are transcriptional repressors. The chronic neurodegeneration-UP signature was further enriched in astrocyte-secreted extracellular matrix proteins (Lama4, Cyr61, Thbs4), while the DOWN signature included relevant genes such as Agl (glycogenolysis), S1pr1 (immune modulation), and Sod2 (anti-oxidant). Only the pan-injury-UP mouse signature was clearly present in some human neurodegenerative transcriptomic datasets.

Conclusions
Acute and chronic CNS injuries lead to distinct astrocyte gene expression programs beyond their common astrocyte reaction signature. However, caution should be taken when extrapolating astrocyte transcriptomic findings from mouse models to human diseases.
Sirt6 inhibition delays the onset of experimental autoimmune encephalomyelitis by reducing dendritic cell migration
Authors: Ferrara Giovanni , Benzi Andrea , Sturla Laura , Marubbi Daniela , Frumento Davide , Spinelli Sonia , Abbotto Elena , Ivaldi Federico , von Holtey Maria , Murone Maximilien , Nencioni Alessio , Uccelli Antonio , Bruzzone Santina 
Published: July 2020

AbstractBackgroundExperimental autoimmune encephalomyelitis (EAE) is the most common animal model of multiple sclerosis (MS), a neuroinflammatory and demyelinating disease characterized by multifocal perivascular infiltrates of immune cells. Although EAE is predominantly considered a T helper 1-driven autoimmune disease, mounting evidence suggests that activated dendritic cells (DC), which are the bridge between innate and adaptive immunity, also contribute to its pathogenesis. Sirtuin 6 (SIRT6), a NAD+-dependent deacetylase involved in genome maintenance and in metabolic homeostasis, regulates DC activation, and its pharmacological inhibition could, therefore, play a role in EAE development.MethodsEAE was induced in female C57bl/6 mice by MOG35-55 injection. The effect of treatment with a small compound SIRT6 inhibitor, administered according to therapeutic and preventive protocols, was assessed by evaluating the clinical EAE score. SIRT6 inhibition was confirmed by Western blot analysis by assessing the acetylation of histone 3 lysine 9, a known SIRT6 substrate. The expression of DC activation and migration markers was evaluated by FACS in mouse lymph nodes. In addition, the expression of inflammatory and anti-inflammatory cytokines in the spinal cord were assessed by qPCR. T cell infiltration in spinal cords was evaluated by immunofluorescence imaging. The effect of Sirt6 inhibition on the migration of resting and activated bone marrow-derived dendritic cells was investigated in in vitro chemotaxis assays.ResultsPreventive pharmacological Sirt6 inhibition effectively delayed EAE disease onset through a novel regulatory mechanism, i.e., by reducing the representation of CXCR4-positive and of CXCR4/CCR7-double-positive DC in lymph nodes. The delay in EAE onset correlated with the early downregulation in the expression of CD40 on activated lymph node DC, with increased level of the anti-inflammatory cytokine IL-10, and with a reduced encephalitogenic T cell infiltration in the central nervous system. Consistent with the in vivo data, in vitro pharmacological Sirt6 inhibition in LPS-stimulated, bone marrow-derived DC reduced CCL19/CCL21- and SDF-1-induced DC migration.ConclusionsOur findings indicate the ability of Sirt6 inhibition to impair DC migration, to downregulate pathogenic T cell inflammatory responses and to delay EAE onset. Therefore, Sirt6 might represent a valuable target for developing novel therapeutic agents for the treatment of early stages of MS, or of other autoimmune disorders.
Chronic extradural compression of spinal cord leads to syringomyelia in rat model
Authors: Ma Longbing , Yao Qingyu , Zhang Can , Li Mo , Cheng Lei , Jian Fengzeng 
Published: July 2020

Abstract
Background
Syringomyelia is a common spinal cord lesion. However, whether CSF blockage is linked to the formation and enlargement of syringomyelia is still controversial. The current model of syringomyelia needs modification to more closely mimic the clinical situation.

Methods
We placed cotton strips under the T13 lamina of 40 8-week-old rats and blocked CSF flow by extradural compression. After 4 and 8 weeks, MRI was performed to evaluate the morphology of syringomyelia and the ratio of spinal cord diameter to syrinx diameter calculated. Locomotor function was evaluated weekly. Spinal cord sections, staining and immunohistochemistry were performed 8 weeks after surgery, the ratio of the central canal to the spinal cord area was calculated, and ependymal cells were counted. In another experiment, we performed decompression surgery for 8 rats with induced syringomyelia at the 8th week after surgery. During the surgery, the cotton strip was completely removed without damaging the dura mater. Then, the rats received MRI imaging during the following weeks and were sacrificed for pathological examination at the end of the experiment.

Results
Syringomyelia formed in 82.5% (33/40) of rats at the 8-week follow-up. The Basso, Beattie and Bresnahan (BBB) scores of rats in the experimental group decreased from 21.0±0.0 to 18.0 ±3.9 in the first week after operation but returned to normal in later weeks. The BBB score indicated that the locomotor deficit caused by compression is temporary and can spontaneously recover. MRI showed that the syrinx is located in the center of the spinal cord, which is very similar to the most common syringomyelia in humans. The ratio of the central canal to the spinal cord area reached (2.9 ± 2.0) × 10−2, while that of the sham group was (5.4 ± 1.5) × 10−4. The number of ependymal cells lining the central canal was significantly increased (101.9 ±  39.6 vs 54.5 ± 3.4). There was no syrinx or proliferative inflammatory cells in the spinal cord parenchyma. After decompression, the syringomyelia size decreased in 50% (4/8) of the rats and increased in another 50% (4/8).

Conclusion
Extradural blockade of CSF flow can induce syringomyelia in rats. Temporary locomotor deficit occurred in some rats. This reproducible rat model of syringomyelia, which mimics syringomyelia in humans, can provide a good model for the study of disease mechanisms and therapies.
A robust spectral angle index for remotely assessing soybean canopy chlorophyll content in different growing stages
Authors: Yue Jibo , Feng Haikuan , Tian Qingjiu , Zhou Chengquan 
Published: July 2020

Abstract
Background
Timely and accurate estimates of canopy chlorophyll (Chl) a and b content are crucial for crop growth monitoring and agricultural management. Crop canopy reflectance depends on many factors, which can be divided into the following categories: (i) leaf effects (e.g., leaf pigments), (ii) canopy effects (e.g., Leaf Area Index [LAI]), and (iii) soil background reflectance (e.g., soil reflectance). The estimation of leaf variables, such as Chl contents, from reflectance at the canopy scale is usually less accurate than that at the leaf scale. In this study, we propose a Visible and Near-infrared (NIR) Angle Index (VNAI) to estimate the Chl content of soybean canopy, and soybean canopy Chl maps are produced using visible and NIR unmanned aerial vehicle (UAV) remote sensing images. The VNAI is insensitive to LAI and can be used for the multi-stage estimation of crop canopy Chl content.

Results
Eleven previously used vegetation indices (VIs) (e.g., Pigment-specific Normalized Difference Index) were selected for performance comparison. The results showed that (i) most previously used Chl VIs were significantly correlated with LAI, and the proposed VNAI was more sensitive to Chl content than LAI; (ii) the VNAI-based estimates of Chl content were more accurate than those based on the other investigated VIs using (1) simulated, (2) real (field), and (3) real (UAV) datasets.

Conclusions
Most previously used Chl VIs were significantly correlated with LAI whereas the proposed VNAI was more sensitive to Chl content than to LAI, indicating that the VNAI may be more strongly correlated with Chl content than these previously used VIs. Multi-stage estimations of the Chl content of cropland obtained using the VNAI and broadband remote sensing images may help to obtain Chl maps with high temporal and spatial resolution.
THEMS: an automated thermal and hyperspectral proximal sensing system for canopy reflectance, radiance and temperature
Authors: Woodgate William , van Gorsel Eva , Hughes Dale , Suarez Lola , Jimenez-Berni Jose , Held Alex 
Published: July 2020

Abstract
Background
Earth Observation ‘EO’ remote sensing technology development enables original insights into vegetation function and health at ever finer temporal, spectral and spatial resolution. Research sites equipped with monitoring infrastructure such as flux towers operate at a key bridging scale between satellite platform measurements and on-the-ground leaf-level processes.

Results
This paper presents the technical details of the design and operation of a proximal observation system ‘THEMS’ that generates unattended long-term high quality thermal and hyperspectral images of a forest canopy on a short (sub-daily) timescale. The primary purpose of the system is to measure canopy temperature, spectral reflectance and radiance coincident with a highly instrumented flux tower site for benchmarking purposes. Basic system capability is demonstrated through low level data product descriptions of the high-resolution multi-angular imagery and ancillary data streams. The system has been successfully operational for more than 2 years with little to no intervention.

Conclusions
These data can then be used to derive remotely sensed proxies of canopy and ecosystem function to study temporal forest dynamics over a wide range of wavelengths, spatial scales (individual trees to canopy), and temporal scales (minutes to multiple years). The multi-purpose system is intended to provide unprecedented spatio-temporal ecophysiological insight and to underpin upscaling of remotely sensed dynamic ecosystem water, CO2, and energy exchange processes.
Analysis of risk factors in thoracic trauma patients with a comparison of a modern trauma centre: a mono-centre study
Authors: Beshay Morris , Mertzlufft Fritz , Kottkamp Hans Werner , Reymond Marc , Schmid Ralph Alexander , Branscheid Detlev , Vordemvenne Thomas 
Published: July 2020

Abstract

Objectives
Thoracic trauma (TT) is the third most common cause of death after abdominal injury and head trauma in polytrauma patients. Its management is still a very challenging task. The purpose of this study was to analyse the risk factors affecting the outcome in a high-volume trauma centre and the efficacy of a specialised trauma team in level 1 trauma centres.

Patients and methods
Between January 2003 and December 2012, data of all patients admitted to the accident and emergency (A&E) department were prospectively collected at the German Trauma Registry (GTR) and thereafter retrospectively analysed.
Patients with chest trauma, an Injury Severity Score (ISS) ≥ 18 and an Abbreviated Injury Scale (AIS) > 2 in more than one body region were included. Patients were divided into two groups: group I included patients presenting with thoracic trauma between January 2003 and December 2007. The results of this group were compared with the results of another group (group II) in a later 5-year period (Jan. 2008–Dec. 2012). Univariate and multivariate analyses were performed, and differences with p < 0.05 were considered statistically significant.

Results
There were 630 patients (56%) with thoracic trauma. A total of 540 patients (48%) had associated extrathoracic injuries. Group I consisted of 285 patients (197 male, mean age 46 years). Group II consisted of 345 patients (251 male, mean age 49 years). Overall 90-day mortality was 17% (n = 48) in group I vs. 9% (n = 31) in group II (p = 0.024). Complication rates were higher in group I (p = 0.019). Higher Injury Severity Scores (ISSs) and higher Abbreviated Injury Acale (AIS) scores in the thoracic region yielded a higher rate of mortality (p < 0.0001). Young patients (< 40 years) were frequently exposed to severe thoracic injury but showed lower mortality rates (p = 0.014). Patients with severe lung contusions (n = 94) (15%) had higher morbidity and mortality (p < 0.001). Twenty-three (8%) patients underwent emergency thoracotomy in group I vs. 14 patients (4%) in group II (p = 0.041). Organ replacement procedures were needed in 18% of patients in group I vs. 31% of patients in group II (p = 0.038).

Conclusions
The presence of severe lung contusion, a higher ISS and AISthoracic score and advanced age are independent risk factors that are directly related to a higher mortality rate. Management of blunt chest trauma with corrective chest tube insertion, optimal pain control and chest physiotherapy results in good outcomes in the majority of patients. Optimal management with better survival rates is achievable in specialised centres with multidisciplinary teamwork and the presence of thoracic surgical experience.
A surgical reduction technique for posterior cruciate ligament avulsion fracture in total knee arthroplasty: a comparison study
Authors: Lin Wei , Niu Jinghui , Dai Yike , Zhang Huaxing , Zhu Jing , Wang Fei 
Published: July 2020

Abstract
Background
Posterior cruciate ligament (PCL) avulsion fracture of the tibia is an uncommon but serious complication during primary cruciate-retaining total knee arthroplasty (TKA). The first objective of this report was to conduct a retrospective cohort study to investigate the incidence and potential risk factors of PCL avulsion fracture in primary cruciate-retaining TKA. The second objective was to assess the functional outcomes of the knee after reduction of PCL avulsion fracture.

Methods
From January 2014 to January 2016, 56 patients who experienced PCL avulsion fracture of the tibia in primary cruciate-retaining TKA were included in the study group. Patients in this group underwent reduction of avulsion fracture. In this period, we selected 224 patients (control group) for comparison. Patients in this group also underwent the same TKA, but no PCL avulsion fracture occurred. The range of motion of the knee and Knee Society Scores were assessed. The Forgotten Joint Score was used to analyze the ability to forget the joint. Differences were considered statistically significant at p < 0.05.

Results
In our series, the incidence of PCL avulsion fracture was 4.6%. There were no significant differences (p > 0.05) with regard to the preoperative or postoperative range of motion of the knee, final 4-year mean clinical score in the study and control groups 92.4 ± 2.7 and 93.6 ± 1.9, respectively, and mean functional scores of 85.1 ± 1.8 and 87.1 ± 1.2, respectively.

Conclusions
The incidence of PCL avulsion fracture of the tibia is relatively high. Older age and female gender were the two risk factors of fracture in primary cruciate-retaining TKA. Reduction of PCL avulsion fracture with a high-strength line can achieve good stability and function of the knee.
Increases in soil and woody biomass carbon stocks as a result of rangeland riparian restoration
Authors: Matzek Virginia , Lewis David , O’Geen Anthony , Lennox Michael , Hogan Sean D. , Feirer Shane T. , Eviner Valerie , Tate Kenneth W. 
Published: July 2020

AbstractBackgroundGlobally, vegetation in riparian zones is frequently the target of restoration efforts because of its importance in reducing the input of eroded sediment and agricultural nutrient runoff to surface waters. Here we examine the potential of riparian zone restoration to enhance carbon sequestration. We measured soil and woody biomass carbon stocks, as well as soil carbon properties, in a long-term chronosequence of 42 streambank revegetation projects in northern California rangelands, varying in restoration age from 1 to 45 years old.ResultsWhere revegetation was successful, we found that soil carbon measured to 50 cm depth increased at a rate of 0.87 Mg C ha−1year−1on the floodplain and 1.12 Mg C ha−1year−1on the upper bank landform. Restored sites also exhibited trends toward increased soil carbon permanence, including an increased C:N ratio and lower fulvic acid: humic acid ratio. Tree and shrub carbon in restored sites was modeled to achieve a 50-year maximum of 187.5 Mg C ha−1in the channel, 279.3 Mg ha−1in the floodplain, and 238.66 Mg ha−1on the upper bank. After 20 years of restoration, the value of this carbon at current per-ton C prices would amount to $US 15,000 per km of restored stream.ConclusionWe conclude that revegetating rangeland streambanks for erosion control has a substantial additional benefit of mitigating global climate change, and should be considered in carbon accounting and any associated financial compensation mechanisms.
Multisystemic manifestations in a cohort of 75 classical Ehlers-Danlos syndrome patients: natural history and nosological perspectives
Authors: Ritelli Marco , Venturini Marina , Cinquina Valeria , Chiarelli Nicola , Colombi Marina 
Published: July 2020

AbstractBackgroundThe Ehlers-Danlos syndromes (EDS) are rare connective tissue disorders consisting of 13 subtypes with overlapping features including joint hypermobility, skin and generalized connective tissue fragility. Classical EDS (cEDS) is principally caused by heterozygousCOL5A1orCOL5A2variants and rarely by theCOL1A1p.(Arg312Cys) substitution. Current major criteria are (1) skin hyperextensibility plus atrophic scars and (2) generalized joint hypermobility (gJHM). Minor criteria include additional mucocutaneous signs, epicanthal folds, gJHM complications, and an affected first-degree relative. Minimal criteria prompting molecular testing are major criterion 1 plus either major criterion 2 or 3 minor criteria. In addition to these features, the clinical picture also involves multiple organ systems, but large-scale cohort studies are still missing. This study aimed to investigate the multisystemic involvement and natural history of cEDS through a cross-sectional study on a cohort of 75 molecularly confirmed patients evaluated from 2010 to 2019 in a tertiary referral center. The diagnostic criteria, additional mucocutaneous, osteoarticular, musculoskeletal, cardiovascular, gastrointestinal, uro-gynecological, neuropsychiatric, and atopic issues, and facial/ocular features were ascertained, and feature rates compared by sex and age.ResultsOur study confirms that cEDS is mainly characterized by cutaneous and articular involvement, though none of their hallmarks was represented in all cases and suggests a milder multisystemic involvement and a more favorable natural history compared to other EDS subtypes. Abnormal scarring was the most frequent and characteristic sign, skin hyperextensibility and gJHM were less common, all without any sex and age bias; joint instability complications were more recurrent in adults. Some orthopedic features showed a high prevalence, whereas the other issues related to the investigated organ systems were less recurrent with few exceptions and age-related differences.ConclusionsOur findings define the diagnostic relevance of cutaneous and articular features and additional clinical signs associated to cEDS. Furthermore, our data suggest an update of the current EDS nosology concerning scarring that should be considered separately from skin hyperextensibility and that the clinical diagnosis of cEDS may be enhanced by the accurate evaluation of orthopedic manifestations at all ages, faciocutaneous indicators in children, and some acquired traits related to joint instability complications, premature skin aging, and patterning of abnormal scarring in older individuals.