julilili42/papers huggingface dataset:
The Sonic Hedgehog Signaling and Its Components in Recurrent Chordoma of the Spine
2021-09-30

Objective Chordomas are uncommon primary malignant tumours that have a high rate of recurrence. They are thought to form along the spine from remains of the embryonic notochord. Treatment for recurrent tumours is complicated and contentious. They are unresponsive to conventional chemotherapy and radiotherapy. Chordomomas simply lack a viable chemotherapeutic standard. Throughout the fetus's development, the Sonic Hedgehog (SHH) pathways connecting a variety of processes involved in tissue and organ expansion and differentiation. To investigate the role of signalling the hedgehog in recurrent spinal chordomas, immunohistochemistry was used to identify SHH and GLI1 levels. In situ hybridization was also used to differentiate PTCH1 and GLI1 expressions. Methods From 1997 to 2020, we looked at 23 paraffin-embedded recurrent spinal chordoma samples from 23 patients (9 men, 14 women; median age: 63 years). All the patients were treated at the University Medical Center Goettingen in Germany and Azad University of Medical Sciences in Tehran, Iran. This study only included patients who had been diagnosed with conventional chordoma. Results SHH expression (+) and GLI1 expression were discovered in all 23 cases (+) immunohistochemically. GLI1 and SHH levels were markedly increased by recurrent spinal chordoma scores. In the recurrent spinal chordoma, in situ hybridization demonstrated positive responses for PTCH1 and GLI1. Conclusion The Shh sample that represents is believed to play a role in spinal chordoma recurrence. The increased amounts of SHH and GLI1 activity in all chordoma samples, according to the study, indicate an autocrine ligand-dependent activation of the conventional HH signalling cacade. It's hard to rule out a non-canonical or paracrine pathway. Hedgehoginhibitors, such as SHH- and GLl-inhibitors, are believed to be associated in our findings, could be a promising approach for treating recurrent spinal chordomas.
Roadmap on organic–inorganic hybrid perovskite semiconductors and devices
2021-10-01

Metal halide perovskites are the first solution processed semiconductors that can compete in their functionality with conventional semiconductors, such as silicon. Over the past several years, perovskite semiconductors have reported breakthroughs in various optoelectronic devices, such as solar cells, photodetectors, light emitting and memory devices, and so on. Until now, perovskite semiconductors face challenges regarding their stability, reproducibility, and toxicity. In this Roadmap, we combine the expertise of chemistry, physics, and device engineering from leading experts in the perovskite research community to focus on the fundamental material properties, the fabrication methods, characterization and photophysical properties, perovskite devices, and current challenges in this field. We develop a comprehensive overview of the current state-of-the-art and offer readers an informed perspective of where this field is heading and what challenges we have to overcome to get to successful commercialization.
COVID-19 and Cardiac Arrhythmias
2021-10-01

Abstract Since the coronavirus disease (COVID-19) pandemic spread unrelentingly all over the world, millions of cases have been reported. Despite a high number of asymptomatic cases, the course of the disease can be serious or even fatal. The affection of the myocardium, called myocardial injury, is caused by multiple triggers. The occurrence of cardiac arrhythmias in COVID-19 patients with myocardial involvement and a critical course is common. In this review, potential mechanisms, incidence, and treatment options for cardiac arrhythmias in COVID-19 patients will be provided by performing a literature research in MESH database and the National Library of Medicine. Common cardiac arrhythmias in COVID-19 patients were sinus tachycardia, atrial fibrillation (AF), ventricular tachycardia (VT), ventricular fibrillation (VF), atrioventricular block, sinusoidal block or QTc prolongation. AF was the most common heart rhythm disorder. About 10% of COVID-19 patients develop new-onset AF and 23 to 33% showed recurrence of AF in patients with known AF. One retrospective trial revealed the incidence of VT or VF to be 5.9% in hospitalized patients. Both AF and VT are clearly associated with worse outcome. Several mechanisms such as hypoxia, myocarditis, myocardial ischemia, or abnormal host immune response, which induce cardiac arrhythmias, have been described. The effect of QT-prolonging drugs in inducing cardiac arrhythmias has become mitigated as these medications are no longer recommended. Acute management of cardiac arrhythmias in COVID-19 patients is affected by the reduction of exposure of health care personnel. More prospective data are desirable to better understand pathophysiology and consecutively adapt management.
Influence of axial limb rotation on radiographic lower limb alignment: a systematic review
2021-10-01

Abstract Introduction The influence of limb malrotation on long-leg radiographs (LLR) is frequently discussed in literature. This systematic review aimed to describe the influence of limb rotation on alignment measurements alone and in combination with knee flexion, and determine its clinical impact. Materials and methods A literature search was conducted in June 2021 using the databases MEDLINE, Cochrane, Web of Science (Clarivate Analytics), and Embase. The search term ((radiograph OR X-ray) AND (position OR rotation) AND limb alignment) was used. Database query, record screening, and study inclusion and exclusion were performed by two reviewers independently. Experimental studies (using either specimens or synthetic bones) or clinical studies (prospective or retrospective using radiographs of patients) analyzing the influence of limb rotation on anatomic and mechanical limb alignment measurements were included. Characteristics and results of the included studies were summarized, simplified, and grouped for comparison to answer the research question. Studies were compared descriptively, and no meta-analysis was performed. Results A total of 22 studies were included showing large heterogeneity, comprising studies with cadavers, patients, and synthetic bones. Most studies (7 out of 8) reported that external rotation (ER) causes less apparent valgus and leads to more varus and internal rotation (IR) causes more valgus and leads to less varus. However, there is no consensus on the extent of rotation influencing alignment measures. Studies reported about an average change of &gt; 2° ( n = 4) and &lt; 2° ( n = 4) hip-knee-ankle angle (HKA) between 15°IR and 15°ER. There is a consensus that the impact of rotation on mechanical alignment is higher if additional sagittal knee angulation, such as knee flexion, is present. All five studies analyzing the influence of rotation combined with knee flexion (5°–15°) showed an HKA change of &gt; 2° between 15°IR and 15°ER. Conclusion Malrotation is frequently present on LLR, possibly influencing the measured alignment especially in knees with extension deficit. Surgeons must consider this when measuring and treating deformities (high tibial osteotomy or total knee arthroplasties), and analyzing surgical outcomes. Especially in patients with osteoarthritis with knee extension deficits or postoperative swelling, the effect of malrotation is significantly greater.
Cross-sectional study of parental knowledge, behaviour and anxiety in management of paediatric fever among German parents
2021-10-01

Objectives Fever is a common symptom among children. Parental lack of knowledge about fever could cause anxiety and lead to unnecessary measures to subside fever. There is little evidence about German parents’ knowledge and their fever management. Design A cross-sectional study using a paper-based questionnaire. Setting 16 kindergartens in Saarbrücken and Saarlouis regional association accepted to participate in the study. Parents from these kindergartens were requested during the pickup time to answer the questionnaire. Participants 481 German parents participated in the study, 394 of them were women. Inclusion criteria were good understanding of German and being a parent of at least one child below the age of 7 years. Primary and secondary outcome measures Knowledge and behaviour of parents on paediatric fever management and the factors influencing fever anxiety. Results The older the parents were, the more anxiety they reported. Their definition of fever had a wide range of 30°C–41°C (mean 38.46, SD=0.67) and almost 90% (mean 3.05, SD=2.03) of participants reported fever as useful, whereby they felt more confident the more they found fever useful. 69% of parents felt calm when their child has fever (mean 4.47, SD=2.27). In case of fever, 55% of parents administer paracetamol, 72% ibuprofen and 32% of them would alternate between the two. Paracetamol and ibuprofen are used more by more anxious parents. In explorative factor analysis, reasons to reduce temperature were summarised in three main factors: damage prevention, illness control and well-being protection, whereby the first two were positively related to parental anxiety. Conclusions Both knowledge as well as level of confidence/anxiety vary largely. Taking antipyretics is related to higher level of anxiety, indicating the need for further education. Fever anxiety depends on multiple factors, which have to be further investigated.
NeRD: Neural Reflectance Decomposition from Image Collections
2021-10-01

Decomposing a scene into its shape, reflectance, and illumination is a challenging but important problem in computer vision and graphics. This problem is inherently more challenging when the illumination is not a single light source under laboratory conditions but is instead an unconstrained environmental illumination. Though recent work has shown that implicit representations can be used to model the radiance field of an object, most of these techniques only enable view synthesis and not relighting. Additionally, evaluating these radiance fields is resource and time-intensive. We propose a neural reflectance decomposition (NeRD) technique that uses physically-based rendering to decompose the scene into spatially varying BRDF material properties. In contrast to existing techniques, our input images can be captured under different illumination conditions. In addition, we also propose techniques to convert the learned reflectance volume into a relightable textured mesh enabling fast real-time rendering with novel illuminations. We demonstrate the potential of the proposed approach with experiments on both synthetic and real datasets, where we are able to obtain high-quality relightable 3D assets from image collections. The datasets and code is available on the project page: https://markboss.me/publication/2021-nerd/
Artificial intelligence in history education. Linguistic content and complexity analyses of student writings in the CAHisT project (Computational assessment of historical thinking)
2021-10-01

The use of standardized test formats in the assessment of historical competencies has recently come under severe criticism, especially in the United States, where standardized tests are particularly common. History researchers have argued that open-ended items are more appropriate for assessment. However, providing largescale evaluations of open-ended answers is time consuming and poses challenges regarding the objectivity, validity, and replicability of ratings. To address this issue, we investigated the extent to which computer-based evaluation methods are suitable for evaluating student answers by combining qualitative methods from history education research with quantitative, computer-based linguistic analyses. In two studies, we analyzed data from an intervention study in which 962 students (ninth graders) completed seven open-ended tasks. In Study 1, we investigated the extent to which task complexity could be predicted from the linguistic complexity of the students' answers. In Study 2, we conducted an automatic content assessment by aligning student answers with predefined target answers and compared automatic scores with human ratings that were based on an elaborate evaluation scheme we developed. In our first study, we identified several linguistic features of students' answers that successfully predicted task complexity. In our second study, the correlations between manual and computational task scores were encouraging. However, our human interrater agreement left room for improvement and demonstrated the challenges of reliably applying explicit evaluation criteria to open tasks. Overall, our findings illustrate that the combination of qualitative methods from history education research and quantitative computational-linguistic analyses may support the large-scale evaluation of open tasks.
Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors
2021-10-01

Background Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS tumors of infancy and early childhood. Hallmark is the surprisingly simple genome with inactivating mutations or deletions in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expanded T cells. However, it is unclear which epitopes T cells might recognize on AT/RT cells. Methods Here, we report a comprehensive mass spectrometry (MS)-based analysis of naturally presented human leukocyte antigen (HLA) class I and class II ligands on 23 AT/RTs. MS data were validated by matching with a human proteome dataset and exclusion of peptides that are part of the human benignome. Cryptic peptide ligands were identified using Peptide-PRISM. Results Comparative HLA ligandome analysis of the HLA ligandome revealed 55 class I and 139 class II tumor-exclusive peptides. No peptide originated from the SMARCB1 region. In addition, 61 HLA class I tumor-exclusive peptide sequences derived from non-canonically translated proteins. Combination of peptides from natural and cryptic class I and class II origin gave optimal representation of tumor cell compartments. Substantial overlap existed with the cryptic immunopeptidome of glioblastomas, but no concordance was found with extracranial tumors. More than 80% of AT/RT exclusive peptides were able to successfully prime CD8 + T cells, whereas naturally occurring memory responses in AT/RT patients could only be detected for class II epitopes. Interestingly, &gt;50% of AT/RT exclusive class II ligands were also recognized by T cells from glioblastoma patients but not from healthy donors. Conclusions These findings highlight that AT/RTs, potentially paradigmatic for other pediatric tumors with a low mutational load, present a variety of highly immunogenic HLA class I and class II peptides from canonical as well as non-canonical protein sources. Inclusion of such cryptic peptides into therapeutic vaccines would enable an optimized mapping of the tumor cell surface, thereby reducing the likelihood of immune evasion.
Smaller spared subcortical nuclei are associated with worse post-stroke sensorimotor outcomes in 28 cohorts worldwide
2021-10-01

Abstract Up to two-thirds of stroke survivors experience persistent sensorimotor impairments. Recovery relies on the integrity of spared brain areas to compensate for damaged tissue. Deep grey matter structures play a critical role in the control and regulation of sensorimotor circuits. The goal of this work is to identify associations between volumes of spared subcortical nuclei and sensorimotor behaviour at different timepoints after stroke. We pooled high-resolution T1-weighted MRI brain scans and behavioural data in 828 individuals with unilateral stroke from 28 cohorts worldwide. Cross-sectional analyses using linear mixed-effects models related post-stroke sensorimotor behaviour to non-lesioned subcortical volumes (Bonferroni-corrected, P &amp;lt; 0.004). We tested subacute (≤90 days) and chronic (≥180 days) stroke subgroups separately, with exploratory analyses in early stroke (≤21 days) and across all time. Sub-analyses in chronic stroke were also performed based on class of sensorimotor deficits (impairment, activity limitations) and side of lesioned hemisphere. Worse sensorimotor behaviour was associated with a smaller ipsilesional thalamic volume in both early (n = 179; d = 0.68) and subacute (n = 274, d = 0.46) stroke. In chronic stroke (n = 404), worse sensorimotor behaviour was associated with smaller ipsilesional putamen (d = 0.52) and nucleus accumbens (d = 0.39) volumes, and a larger ipsilesional lateral ventricle (d = −0.42). Worse chronic sensorimotor impairment specifically (measured by the Fugl-Meyer Assessment; n = 256) was associated with smaller ipsilesional putamen (d = 0.72) and larger lateral ventricle (d = −0.41) volumes, while several measures of activity limitations (n = 116) showed no significant relationships. In the full cohort across all time (n = 828), sensorimotor behaviour was associated with the volumes of the ipsilesional nucleus accumbens (d = 0.23), putamen (d = 0.33), thalamus (d = 0.33) and lateral ventricle (d = −0.23). We demonstrate significant relationships between post-stroke sensorimotor behaviour and reduced volumes of deep grey matter structures that were spared by stroke, which differ by time and class of sensorimotor measure. These findings provide additional insight into how different cortico-thalamo-striatal circuits support post-stroke sensorimotor outcomes.
Bee products in the prehistoric southern levant: evidence from the lipid organic record
2021-10-01

Beehive products have a rich global history. In the wider Levantine region, bees had a significant role in Egypt and Mesopotamia, and intensive beekeeping was noted in Israel during the Biblical period when apiaries were first identified. This study investigates the origins of this extensive beekeeping through organic residue analysis of pottery from prehistoric sites in the southern Levant. The results suggest that beehive products from likely wild bees were used during the Chalcolithic period as a vessel surface treatment and/or as part of the diet. These functions are reinforced by comparison to the wider archaeological record. While the true frequency of beeswax use may be debated, alternatives to beehive products were seemingly preferred as wild resources contrasted with the socio-economic system centred on domesticated resources, controlled production and standardization. Bee products only became an important part of the economic canon in the southern Levant several millennia later.
Characterization of T cell responses to co-administered hookworm vaccine candidates Na-GST-1 and Na-APR-1 in healthy adults in Gabon
2021-10-01

Two hookworm vaccine candidates, Na-GST-1 and Na-APR-1, formulated with Glucopyranosyl Lipid A (GLA-AF) adjuvant, have been shown to be safe, well tolerated, and to induce antibody responses in a Phase 1 clinical trial (Clinicaltrials.gov NCT02126462) conducted in Gabon. Here, we characterized T cell responses in 24 Gabonese volunteers randomized to get vaccinated three times with Na-GST-1 and Na-APR-1 at doses of 30μg (n = 8) or 100μg (n = 10) and as control Hepatitis B (n = 6). Blood was collected pre- and post-vaccination on days 0, 28, and 180 as well as 2-weeks after each vaccine dose on days 14, 42, and 194 for PBMCs isolation. PBMCs were stimulated with recombinant Na-GST-1 or Na-APR-1, before (days 0, 28 and 180) and two weeks after (days 14, 42 and 194) each vaccination and used to characterize T cell responses by flow and mass cytometry. A significant increase in Na-GST-1 -specific CD4 + T cells producing IL-2 and TNF, correlated with specific IgG antibody levels, after the third vaccination (day 194) was observed. In contrast, no increase in Na-APR-1 specific T cell responses were induced by the vaccine. Mass cytometry revealed that, Na-GST-1 cytokine producing CD4 + T cells were CD161 + memory cells expressing CTLA-4 and CD40-L. Blocking CTLA-4 enhanced the cytokine response to Na-GST-1. In Gabonese volunteers, hookworm vaccine candidate, Na-GST-1, induces detectable CD4 + T cell responses that correlate with specific antibody levels. As these CD4 + T cells express CTLA-4, and blocking this inhibitory molecules resulted in enhanced cytokine production, the question arises whether this pathway can be targeted to enhance vaccine immunogenicity.
Ten reasons why we should not abandon a detailed first trimester anomaly scan
2021-10-01

Within the last two decades, the first trimester screening at 11–13 weeks' gestation has evolved from a simple measurement of the nuchal translucency (NT) thickness and the crown-rump length (CRL) towards a detailed risk stratification for several complications that may happen within the course of the pregnancy [1] [2]. As a consequence, first trimester screening is now considered crucial for the management of each pregnancy. It involves a detailed risk assessment for chromosomal abnormalities, especially for trisomy 21, for preeclampsia and fetal growth restriction as well as a detailed anomaly scan [3] [4] [5] [6] [7] [8] [9]. In a meta-analysis from Karim et al., the detection rate for fetal defects in a high risk population exceeded 60 % [5]. These positive aspects have resulted in the concept of "turning the pyramid of pregnancy care". In short, this model relies on a detailed first trimester risk assessment and stratifies the further management of the pregnancy according to the respective risk profile [10].
Predictive Factors Influencing Functional Results After Proximal Hamstring Tendon Avulsion Surgery: A Patient-Reported Outcome Study After 227 Operations From a Single Center
2021-10-01

Background: Although debilitating, proximal hamstring tendon avulsion injuries are rare and often overlooked or misdiagnosed. Consequently, delayed diagnosis and surgical treatment may result in poor outcomes. Studies investigating a correlation between postoperative functional outcomes and this delay in surgical treatment or other concomitant factors in large cohorts have not yet been performed to our knowledge. Purpose/Hypothesis: The purpose of this study was to conduct an investigation in a large patient group regarding factors that could influence a patient’s functional outcome after hamstring surgery. We hypothesized that this outcome would significantly correlate to the time between trauma and surgery. Study Design: Case series; Level of evidence, 4. Methods: Patients who received surgical treatment of proximal hamstring tendon avulsion injuries in our institution between the years 2010 and 2020 were asked to complete a validated, injury-specific outcome measurement, the Perth Hamstring Assessment Tool (PHAT; 0-100 points). In addition to calculating these outcomes, we evaluated the association of the obtained results with possible predictive factors such as age, sex, stump retraction shown on magnetic resonance imaging (MRI), and timing and duration of surgery. Results: A total of 226 patients (227 operations) were eligible for the study, and 204 cases of hamstring tendon avulsion injury met our inclusion criteria. The return rate for the PHAT questionnaire was 85.3%. The mean PHAT score revealed good results (79.8 ± 19.1). Irrespective of concomitant factors, the scores of male patients were significantly higher compared with those of female patients (83.8 ± 16.9 vs 75.8 ± 20.6 respectively; P = .004). The mean time to surgery was 5.7 weeks after trauma, and more delayed surgery correlated significantly with lower PHAT scores ( P = .003; r = –0.228). The mean degree of stump retraction on MRI (5 cm) did not significantly influence PHAT scores ( P = .525; r = –0.06). Conclusion: Delay of surgery and female sex were disadvantageous in terms of a good functional outcome measure (PHAT score) after hamstring tendon refixation surgery. By contrast, patient age as well as the retraction of the tendon stump on preoperative MRI did not influence PHAT scores in the present study.