julilili42/papers huggingface dataset:
Teacher motivation and student outcomes: Searching for the signal
2021-10-02

Recent years have witnessed a burgeoning interest in the study of teacher motivation. Although links between teacher motivation and teacher well-being, commitment to the profession, and other teacher-related outcomes are well-documented, prior research on associations between teacher motivation and student outcomes has been less consistent. This article focuses on teacher motivation as situated within two prominent frameworks: self-determination theory and achievement goal theory. First, two systematic reviews of research on self-determination theory and achievement goal theory are conducted to examine whether, when, how, and why teachers' motivation may influence—or at least relate to—which student outcomes. The processes by which teacher motivation is associated with student outcomes, such as via specific instructional strategies, are also taken into account. Second, the question of why research on teacher motivation often fails to find consistent effects on student outcomes is considered, including where in the complex chain of events from teacher motivation to student outcomes the signal gets lost. Third, the need to study the reverse ordering of effects, reciprocal effects, and the dynamic interplay between teacher motivation and student outcome variables is discussed.
How competitors become collaborators—Bridging the gap(s) between machine learning algorithms and clinicians
2021-10-02

Abstract For some years, we have been witnessing a steady stream of high‐profile studies about machine learning (ML) algorithms achieving high diagnostic accuracy in the analysis of medical images. That said, facilitating successful collaboration between ML algorithms and clinicians proves to be a recalcitrant problem that may exacerbate ethical problems in clinical medicine. In this paper, we consider different epistemic and normative factors that may lead to algorithmic overreliance within clinical decision‐making. These factors are false expectations, the miscalibration of uncertainties, non‐explainability, and the socio‐technical context within which the algorithms are utilized. Moreover, we identify different desiderata for bridging the gap between ML algorithms and clinicians. Further, we argue that there is an intriguing dialectic in the collaboration between clinicians and ML algorithms. While it is the algorithm that is supposed to assist the clinician in diagnostic tasks, successful collaboration will also depend on adjustments on the side of the clinician.
Current Status and Perspectives on the Application of CRISPR/Cas9 Gene-Editing System to Develop a Low-Gluten, Non-Transgenic Wheat Variety
2021-10-02

Wheat gluten contains epitopes that trigger celiac disease (CD). A life-long strict gluten-free diet is the only treatment accepted for CD. However, very low-gluten wheat may provide an alternative treatment to CD. Conventional plant breeding methods have not been sufficient to produce celiac-safe wheat. RNA interference technology, to some extent, has succeeded in the development of safer wheat varieties. However, these varieties have multiple challenges in terms of their implementation. Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease 9 (CRISPR/Cas9) is a versatile gene-editing tool that has the ability to edit immunogenic gluten genes. So far, only a few studies have applied CRISPR/Cas9 to modify the wheat genome. In this article, we reviewed the published literature that applied CRISPR/Cas9 in wheat genome editing to investigate the current status of the CRISPR/Cas9 system to produce a low-immunogenic wheat variety. We found that in recent years, the CRISPR/Cas9 system has been continuously improved to edit the complex hexaploid wheat genome. Although some reduced immunogenic wheat varieties have been reported, CRISPR/Cas9 has still not been fully explored in terms of editing the wheat genome. We conclude that further studies are required to apply the CRISPR/Cas9 gene-editing system efficiently for the development of a celiac-safe wheat variety and to establish it as a “tool to celiac safe wheat”.
ARTS-DB: a database for antibiotic resistant targets
2021-10-02

Abstract As a result of the continuous evolution of drug resistant bacteria, new antibiotics are urgently needed. Encoded by biosynthetic gene clusters (BGCs), antibiotic compounds are mostly produced by bacteria. With the exponential increase in the number of publicly available, sequenced genomes and the advancements of BGC prediction tools, genome mining algorithms have uncovered millions of uncharacterized BGCs for further evaluation. Since compound identification and characterization remain bottlenecks, a major challenge is prioritizing promising BGCs. Recently, researchers adopted self-resistance based strategies allowing them to predict the biological activities of natural products encoded by uncharacterized BGCs. Since 2017, the Antibiotic Resistant Target Seeker (ARTS) facilitated this so-called target-directed genome mining (TDGM) approach for the prioritization of BGCs encoding potentially novel antibiotics. Here, we present the ARTS database, available at https://arts-db.ziemertlab.com/. The ARTS database provides pre-computed ARTS results for &amp;gt;70,000 genomes and metagenome assembled genomes in total. Advanced search queries allow users to rapidly explore the fundamental criteria of TDGM such as BGC proximity, duplication and horizontal gene transfers of essential housekeeping genes. Furthermore, the ARTS database provides results interconnected throughout the bacterial kingdom as well as links to known databases in natural product research.
Dynamic DNA methylation changes in the COMT gene promoter region in response to mental stress and its modulation by transcranial direct current stimulation
2021-10-02

Abstract Changes in epigenetic modifications present a mechanism how environmental factors like the experience of stress can alter gene regulation. While stress-related disorders have consistently been associated with differential DNA methylation, little is known about the time scale in which these alterations emerge. We investigated dynamic DNA methylation changes in whole blood of 42 healthy male individuals in response to a stressful cognitive task, its association with concentration changes in cortisol and its modulation by transcranial direct current stimulation (tDCS). We observed a continuous increase in COMT promotor DNA methylation which correlated with higher saliva cortisol levels and was still detectable one week later. However, this lasting effect was suppressed by concurrent activity-enhancing anodal tDCS to the dorsolateral prefrontal cortex. Our findings support the significance of gene-specific DNA methylation in whole blood as potential biomarkers for stress-related disorders. Moreover, they suggest alternative molecular mechanisms possibly involved in lasting behavioral effects of tDCS.
Genome report: a draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics
2021-10-02

Abstract The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here, we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara and Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy, and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one-third of BUSCO genes (390/1440) mapped to two or more scaffolds despite &amp;lt;2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.
Tilted 3D visual scenes – A new therapy approach for pusher syndrome
2021-10-02

Abstract Hemiparetic stroke patients with ‘pusher syndrome’ use their non-paretic extremities to push towards their paralyzed side and actively resist external posture correction. The disorder is associated with a distorted perception of postural vertical combined with a maintained, or little deviating perception of visual upright. With the aim of reducing this mismatch, and thus reducing pushing behavior, we manipulated the orientation of visual input in a virtual reality setup. We presented healthy subjects and an acute stroke patient with severe pusher syndrome a 3D visual scene that was either upright or tilted in roll plane by 20°. By moving the sitting participants in roll plane to the left and right, we assessed the occurrence of active pushing behavior, namely the active resistance to external posture manipulation. With the 3D visual scene oriented upright, the patient with pusher syndrome showed the typical active resistance against tilts towards the ipsilesional side. He used his non-paretic arm to block the examiner’s attempt to move the body axis towards that side. With the visual scene tilted to the ipsiversive left, his pathological resistance was significantly reduced. Statistically, the tolerated body tilt angles no longer differed from those of healthy controls. We conclude that even short presentations of tilted 3D visual input can reduce pusher symptoms. The technique provides potential for a new treatment method of pusher syndrome and offers a simple, straightforward approach that can be effortlessly integrated in clinical practice.
Diachronic Changes of Frequencies in Discourse Connectives in English: Evidence from COHA
2021-10-02

Recent studies have claimed that the amount of discourse connectives or discourse markers has risen in multiple languages. However, the thesis has seldom been evaluated using comprehensive empirical data evidence. This study investigates the historical changes of frequencies in discourse connectives in the English language over the last two hundred years. We find that the frequencies of the majority of discourse connectives showed a marked decrease. An opposing trend can be seen with respect to only a few types of discourse connectives. These research results show that the frequencies of discourse markers in English have not in fact increased over the last two centuries. We analyze the possible reasons for this decline. And this result suggests that English language users tend to use explicit discourse connectives less frequently, which finding may challenge recent claims concerning the rise of discourse connectives (markers).
Immunosuppression in Malaria: Do Plasmodium falciparum Parasites Hijack the Host?
2021-10-03

Malaria reflects not only a state of immune activation, but also a state of general immune defect or immunosuppression, of complex etiology that can last longer than the actual episode. Inhabitants of malaria-endemic regions with lifelong exposure to the parasite show an exhausted or immune regulatory profile compared to non- or minimally exposed subjects. Several studies and experiments to identify and characterize the cause of this malaria-related immunosuppression have shown that malaria suppresses humoral and cellular responses to both homologous (Plasmodium) and heterologous antigens (e.g., vaccines). However, neither the underlying mechanisms nor the relative involvement of different types of immune cells in immunosuppression during malaria is well understood. Moreover, the implication of the parasite during the different stages of the modulation of immunity has not been addressed in detail. There is growing evidence of a role of immune regulators and cellular components in malaria that may lead to immunosuppression that needs further research. In this review, we summarize the current evidence on how malaria parasites may directly and indirectly induce immunosuppression and investigate the potential role of specific cell types, effector molecules and other immunoregulatory factors.
Antibody-mediated depletion of human CLEC-2 in a novel humanised mouse model
2021-10-03

Abstract Platelet C-type lectin-like receptor 2 (CLEC-2) has been proposed as a potential anti-thrombotic target as genetic or antibody-mediated receptor deficiency prevents occlusive thrombus formation in mice. This occurs through interaction with an unknown ligand as the endogenous ligand podoplanin is not present in the vasculature. However, the CLEC-2-podoplanin interaction does have an important role in tumour metastasis. There are currently no methods to test potential human therapeutics targeting CLEC-2, such as antibodies, in vivo . We have therefore generated and characterised a humanised CLEC-2 mouse (hCLEC-2 KI ) and developed a novel monoclonal anti-human CLEC-2 antibody, HEL1, for in vivo testing. hCLEC-2 KI mice were phenotypically normal and had comparable platelet glycoprotein receptor expression, activation and aggregation to wildtype platelets. hCLEC-2 KI mice had both comparable bleeding and vessel occlusion times to WT mice. Challenging hCLEC-2 KI mice with HEL1 or a second monoclonal anti-hCLEC-2 antibody, AYP1, resulted in transient thrombocytopenia as well as CLEC-2 depletion for more than 2 weeks but had no effect on haemostasis. This illustrates the power of the humanised CLEC-2 mouse model in evaluating novel therapeutics in vivo , including antibodies that target CLEC-2, as well as the limited effect on haemostasis when targeting CLEC-2.
Disrupting Short-Term Memory Maintenance in Premotor Cortex Affects Serial Dependence in Visuomotor Integration
2021-10-04

Human behavior is biased by past experience. For example, when intercepting a moving target, the speed of previous targets will bias responses in future trials. Neural mechanisms underlying this so-called serial dependence are still under debate. Here, we tested the hypothesis that the previous trial leaves a neural trace in brain regions associated with encoding task-relevant information in visual and/or motor regions. We reasoned that injecting noise by means of transcranial magnetic stimulation (TMS) over premotor and visual areas would degrade such memory traces and hence reduce serial dependence. To test this hypothesis, we applied bursts of TMS pulses to right visual motion processing region hV5/MT+ and to left dorsal premotor cortex (PMd) during intertrial intervals of a coincident timing task performed by twenty healthy human participants (15 female). Without TMS, participants presented a bias toward the speed of the previous trial when intercepting moving targets. TMS over PMd decreased serial dependence in comparison to the control Vertex stimulation, whereas TMS applied over hV5/MT+ did not. In addition, TMS seems to have specifically affected the memory trace that leads to serial dependence, as we found no evidence that participants' behavior worsened after applying TMS. These results provide causal evidence that an implicit short-term memory mechanism in premotor cortex keeps information from one trial to the next, and that this information is blended with current trial information so that it biases behavior in a visuomotor integration task with moving objects. SIGNIFICANCE STATEMENT Human perception and action are biased by the recent past. The origin of such serial bias is still not fully understood, but a few components seem to be fundamental for its emergence: the brain needs to keep previous trial information in short-term memory and blend it with incoming information. Here, we present evidence that a premotor area has a potential role in storing previous trial information in short-term memory in a visuomotor task and that this information is responsible for biasing ongoing behavior. These results corroborate the perspective that areas associated with processing information of a stimulus or task also participate in maintaining that information in short-term memory even when this information is no longer relevant for current behavior.
The potential of relevance interventions for scaling up: A cluster-randomized trial testing the effectiveness of a relevance intervention in math classrooms.
2021-10-04

Relevance interventions have shown a great potential to foster motivation and achievement (Lazowski & Hulleman, 2016). Yet, further research is warranted to test how such interventions can be successfully implemented in practice. We conducted a cluster-randomized trial in ninth-grade math classrooms to test the effectiveness of a relevance intervention, which was shown to be efficacious when implemented by researchers, for fostering motivation and achievement under real-world conditions. The 78 participating classrooms (N = 1,744 students) were randomly assigned to one of two intervention conditions or a waitlist control condition. The intervention was implemented by master’s students or the regular math teachers. Intervention effects were evaluated using self-reports, teacher ratings, and achievement tests 4 weeks and 3 months after the intervention, controlling for the initial levels of the outcomes. Compared with the control condition, both intervention conditions showed similar positive effects on utility value. Unexpectedly, students in both intervention conditions also reported higher perceived cost compared with students in the control condition after the intervention. When implemented by master’s students, additional intervention effects on students’ growth mindsets and a standardized achievement test could be observed. Only small differences in effectiveness were observed between the intervention conditions, although master’s students showed a higher level of adherence. In both intervention conditions, higher levels of adherence and lower levels of discipline problems were associated with more positive changes in utility value. Overall, the intervention thus showed mixed effects. Future research should therefore continue to examine the conditions under which relevance interventions work in practice. (PsycInfo Database Record (c) 2021 APA, all rights reserved)
Combined Molecular and Elemental Mass Spectrometry Approaches for Absolute Quantification of Proteomes: Application to the Venomics Characterization of the Two Species of Desert Black Cobras, Walterinnesia aegyptia and Walterinnesia morgani
2021-10-04

We report a novel hybrid, molecular and elemental mass spectrometry (MS) setup for the absolute quantification of snake venom proteomes shown here for two desert black cobra species within the genus <i>Walterinnesia</i>, <i>Walterinnesia aegyptia</i> and <i>Walterinnesia morgani</i>. The experimental design includes the decomplexation of the venom samples by reverse-phase chromatography independently coupled to four mass spectrometry systems: the combined bottom-up and top-down molecular MS for protein identification and a parallel reverse-phase microbore high-performance liquid chromatograph (RP-μHPLC) on-line to inductively coupled plasma (ICP-MS/MS) elemental mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QToF MS). This allows to continuously record the absolute sulfur concentration throughout the chromatogram and assign it to the parent venom proteins separated in the RP-μHPLC-ESI-QToF parallel run via mass profiling. The results provide a locus-resolved and quantitative insight into the three desert black cobra venom proteome samples. They also validate the units of measure of our snake venomics strategy for the relative quantification of snake venom proteomes as % of total venom peptide bonds as a proxy for the % by weight of the venom toxins/toxin families. In a more general context, our work may pave the way for broader applications of hybrid elemental/molecular MS setups in diverse areas of proteomics.
Constraining the Konoplya-Rezzolla-Zhidenko deformation parameters. II. Limits from stellar-mass black hole x-ray data
2021-10-04

Astrophysical black holes are thought to be the Kerr black holes predicted by general relativity, but macroscopic deviations from the Kerr solution can be expected from a number of scenarios involving new physics. In Paper I, we studied the reflection features in NuSTAR and XMM-Newton spectra of the supermassive black hole at the center of the galaxy MCG-06-30-15 and we constrained a set of deformation parameters proposed by Konoplya, Rezzolla & Zhidenko (Phys. Rev. D93, 064015, 2016). In the present work, we analyze the X-ray data of a stellar-mass black hole within the same theoretical framework in order to probe a different curvature regime. We consider a NuSTAR observation of the X-ray binary EXO 1846-031 during its outburst in 2019. As in the case of Paper I, all our fits are consistent with the Kerr black hole hypothesis, but some deformation parameters cannot be constrained well.
ENT Residents Benefit from a Structured Operation Planning Approach in the Training of Functional Endoscopic Sinus Surgery
2021-10-04

Background and Objectives: Preoperative planning utilizing computed tomographies (CT) is of utmost importance in functional endoscopic sinus surgery (FESS). Frequently, no uniform documentation and planning structures are available to residents in training. Consequently, overall completeness and quality of operation planning may vary greatly. The objective of the present study was to evaluate the impact of a structured operation planning (SOP) approach on the report quality and user convenience during a 4-day sinus surgery course. Materials and Methods: Fifteen participant were requested to plan a FESS procedure based on a CT scan of the paranasal sinuses that exhibited common pathological features, in a conventional manner, using a free text. Afterwards, the participants reevaluated the same scans by means of a specifically designed structured reporting template. Two experienced ENT surgeons assessed the collected conventional operation planning (COP) and SOP methods independently with regard to time requirements, overall quality, and legibility. User convenience data were collected by utilizing visual analogue scales. Results: A significantly greater time expenditure was associated with SOPs (183 s vs. 297 s, p = 0.0003). Yet, legibility (100% vs. 72%, p &lt; 0.0001) and overall completeness (61.3% vs. 22.7%, p &lt; 0.0001) of SOPs was significantly superior to COPs. Additionally, description of highly relevant variants in anatomy and pathologies were outlined in greater detail. User convenience data delineated a significant preference for SOPs (VAS 7.9 vs. 6.9, p = 0.0185). Conclusions: CT-based planning of FESS procedures by residents in training using a structured approach is more time-consuming while producing a superior report quality in terms of detailedness and readability. Consequently, SOP can be considered as a valuable tool in the process of preoperative evaluations, especially within residency.