Miracle-dz/UniFAR-FTUs huggingface dataset:
Neurite outgrowth inhibitor Nogo-A establishes spatial segregation and extent of oligodendrocyte myelination

A requisite component of nervous system development is the achievement of cellular recognition and spatial segregation through competition-based refinement mechanisms. Competition for available axon space by myelinating oligodendrocytes ensures that all relevant CNS axons are myelinated properly. To ascertain the nature of this competition, we generated a transgenic mouse with sparsely labeled oligodendrocytes and establish that individual oligodendrocytes occupying similar axon tracts can greatly vary the number and lengths of their myelin internodes. Here we show that intercellular interactions between competing oligodendroglia influence the number and length of myelin internodes, referred to as myelinogenic potential, and identify the amino-terminal region of Nogo-A, expressed by oligodendroglia, as necessary and sufficient to inhibit this process. Exuberant and expansive myelination/remyelination is detected in the absence of Nogo during development and after demyelination, suggesting that spatial segregation and myelin extent is limited by microenvironmental inhibition. We demonstrate a unique physiological role for Nogo-A in the precise myelination of the developing CNS. Maximizing the myelinogenic potential of oligodendrocytes may offer an effective strategy for repair in future therapies for demyelination.
Autogenic Training Alters Cerebral Activation Patterns in fMRI

Abstract Cerebral activation patterns during the first three auto-suggestive phases of autogenic training (AT) were investigated in relation to perceived experiences. Nineteen volunteers trained in AT and 19 controls were studied with fMRI during the first steps of autogenic training. FMRI revealed activation of the left postcentral areas during AT in those with experience in AT, which also correlated with the level of AT experience. Activation of prefrontal and insular cortex was significantly higher in the group with experience in AT while insular activation was correlated with number years of simple relaxation exercises. Specific activation in subjects experienced in AT may represent a training effect. Furthermore, the correlation of insular activation suggests that these subjects are different from untrained subjects in emotional processing or self-awareness.
How Video Rental Patterns Change as Consumers Move Online

How will consumption patterns for popular and “long-tail” products change when consumers move from brick-and-mortar to Internet markets? We address this question using customer-level panel data obtained from a national video rental chain as it was closing many of its local stores. These data allow us to use the closure of a consumer's local video store as an instrument, breaking the inherent endogeneity between channel choice and product choice. Our results suggest that when consumers move from brick-and-mortar to online channels, they are significantly more likely to rent “niche” titles relative to “blockbusters. ” This suggests that a significant amount of niche product consumption online is due to the direct influence of the channel on consumer behavior, not just due to selection effects from the types of consumers who decide to use the Internet channel or the types of products that consumers decide to purchase online. This paper was accepted by Pradeep Chintagunta, marketing.
The grape berry-specific basic helix–loop–helix transcription factor VvCEB1 affects cell size

The development of fleshy fruits involves complex physiological and biochemical changes. After fertilization, fruit growth usually begins with cell division, continues with both cell division and expansion, allowing fruit set to occur, and ends with cell expansion only. In spite of the economical importance of grapevine, the molecular mechanisms controlling berry growth are not fully understood. The present work identified and characterized Vitis vinifera cell elongation bHLH protein (VvCEB1), a basic helix–loop–helix (bHLH) transcription factor controlling cell expansion in grape. VvCEB1 was expressed specifically in berry-expanding tissues with a maximum around veraison. The study of VvCEB1 promoter activity in tomato confirmed its specific fruit expression during the expansion phase. Overexpression of VvCEB1 in grape embryos showed that this protein stimulates cell expansion and affects the expression of genes involved in cell expansion, including genes of auxin metabolism and signalling. Taken together, these data show that VvCEB1 is a fruit-specific bHLH transcription factor involved in grape berry development.
Programming Misconceptions in an Introductory Level Programming Course Exam

Learning to program is known to be a difficult task, as the students typically lack the intrinsic motivation and find the new skills required difficult to master. It is hence typical for the educators to try to constantly improve their teaching methods to enhance the quality and outcome of the courses. We have developed an educational tool called ViLLE, which allows us to create interactive and automatically assessed programming exercises easily. In these exercises, the students have a near-to-authentic programming environment with compiler output and error messages provided. The same tool was used in our university's introductory programming course's final exam. In this paper, we analyze students' answers to three different coding exercises in this final exam. Since ViLLE automatically stores the program code when compiled, we have an access to previously unseen amounts of iterations of the exercise instead of just the final submission. The data is analyzed to identify typical misconceptions in programming exercises, and to show how the students gradually improve their answers based on the results and error messages. Finally, we discuss how the results of the analysis can be utilized to tackle these misconceptions during the course.
Depression in Chronic Rhinosinusitis: A Controlled Cohort Study

Background Depression in patients with chronic rhinosinusitis (CRS) is underdiagnosed but significantly impacts treatment outcomes and health care utilization. Objective To compare undiagnosed depression in a CRS cohort with a healthy, non-CRS control cohort. Methods A case-control study of patients with symptomatic CRS and a non-CRS control cohort was performed. Demographic and comorbidity factors were correlated to depression-specific outcomes by using the Beck Depression Inventory II (BDI). Results We enrolled 42 patients with CRS and 88 control patients with no history of CRS. Physician-diagnosed depression was equivalent in CRS and control patients (6% and 9%, respectively). BDI-detected depression was higher among patients with CRS compared with controls (31% versus 14.8%, respectively; p = 0.031). BDI scores were higher in patients with CRS even when controlling for comorbid asthma, allergy, and aspirin sensitivity. When examined by polyp status, the patients without polyps had more depression than did the controls (38% versus 14.8%; p = 0.048). The somatic subscale scores of the BDI were worse in patients with CRS (p = 0.004), whereas the cognitive subscale trended toward significance (p = 0.081). Conclusion Depression may be more common in CRS than previously recognized, especially in patients without polyps. Somatic subscale scores of the BDI are increased in CRS and may impact future treatment outcomes.
Characterization of a conserved helper-T-cell epitope from group A Streptococcal M proteins

We have previously defined major histocompatibility complex (MHC) class II-restricted T-cell epitopes from the carboxy-terminal region of group A streptococcal type 5 M protein. In this report, T-cell responses to one of these epitopes have been characterized in detail. T-cell clones from recombinant M5-immunized mice and popliteal lymph node cells from peptide-immunized mice were used to show that sM5[300-319] is recognized in the context of I-A alleles of four of nine independent MHC class II haplotypes: I-Ad, I-Af, I-Ak, and I-As. This epitope was also recognized by both helper (Th2) and inflammatory (Th1) subsets of murine T cells. The I-Ad-restricted epitope recognized by BALB/c mice was mapped to the 12-amino-acid peptide sM5[308-319] and was shown to provide helper function for an immunoglobulin G anti-peptide antibody response in BALB/c mice. Anti-peptide antibody was shown to be specific for M5[304-315] but failed to recognize intact rM5, suggesting that the conformation of the epitope differed between peptide and protein. However, the results demonstrate that overlapping epitopes can be the focus for both immunoglobulin G antibodies and the T cells which augment their production. Comparison of the available sequences for M proteins indicated that the T-cell epitope within M5[300-319] was highly conserved between M types and hence may elicit helper function for protective antibody responses to a wide range of M types. T-cell epitopes from conserved regions of M proteins which are recognized in the context of multiple MHC haplotypes have potential for the design of multivalent streptococcal vaccines.
Upper Cambrian faunas from the subsurface Deadwood Formation, Williston Basin, Montana

The Deadwood Formation was cored from the base of the Winnipeg to the Precambrian schist. The upper 347 feet was assigned to the Lower Ordovician, the middle 300 feet to the Upper Cambrian Trempeleauan and Franconian stages and the lower 257 feet to the Dresbachian. BBrachiopods, trilobites, and dendroid graptolites, including 10 new species, are systematically described for each faunal (trilobite) zone. The faunules support physical evidence that eastern Montana was part of a wide coastal shelf during LateCambrian time and that sporadic sedimentation continued across the Upper Cambrian-Lower Ordovician boundary. --V.M. J
Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. Results In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. Conclusions To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the ‘best’ output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies.
A Dialogical Approach to the Creation of New Knowledge in Organizations

Despite several insightful empirical studies on how new knowledge is created in organizations, there is still no satisfactory answer to this question. The purpose of this chapter is to address the question by focusing on direct social interaction. By reinterpreting several organizational examples, as well as findings from organizational knowledge research, the chapter illustrates the process by which new knowledge in organizations originates and develops using a dialogical perspective. When productive, dialogue leads to self-distanciation, namely to individuals taking distance from their customary and unreflective ways of acting as practitioners. Dialogue is productive depending on the extent to which participants engage relationally with one another. When this happens participants are more likely to actively take responsibility both for the joint tasks in which they are involved and for their relationships with others.
Making myelin basic protein -from mRNA transport to localized translation

In the central nervous system (CNS) of most vertebrates, oligodendrocytes enwrap neuronal axons with extensions of their plasma membrane to form the myelin sheath. Several proteins are characteristically found in myelin of which myelin basic protein (MBP) is the second most abundant one after proteolipid protein. The lack of functional MBP in rodents results in a severe hypomyelinated phenotype in the CNS demonstrating its importance for myelin synthesis. Mbp mRNA is transported from the nucleus to the plasma membrane and is translated locally at the axon–glial contact site. Axonal properties such as diameter or electrical activity influence the degree of myelination. As oligodendrocytes can myelinate many axonal segments with varying properties, localized MBP translation represents an important part of a rapid and axon-tailored synthesis machinery. MBP’s ability to compact cellular membranes may be problematic for the integrity of intracellular membranous organelles and can also explain why MBP is transported in oligodendrocytes in the form of an mRNA rather than as a protein. Here we review the recent findings regarding intracellular transport and signaling mechanisms leading to localized translation of Mbp mRNA in oligodendrocytes. More detailed insights into the MBP synthesis pathway are important for a better understanding of the myelination process and may foster the development of remyelination therapies for demyelinating diseases.
Analysis of ocular dominance pattern formation in a high-dimensional self-organizing-map model

Using a distortion measure for the states emerging in self-organizing maps (SOMs) we mathematically analyse a recently proposed high-dimensional map formation model for ocular dominance patterns. We calculate critical values of parameters for ocular dominance states to occur, and we determine how the pattern layout depends on these parameters. The analysis reveals an increase of ocular dominance bandwidth with decreasing correlation, consistent with a recently observed increase of bandwidth in strabismic cats. In subsequent simulations these analytical results are corroborated, irrespective of the specific normalization procedure (multiplicative or subtractive) employed in the simulations.
The Attenuation of Swell Waves by Rain

Within the progressive improvement in wave modeling we focus on the attenuation of swell waves by rain. Till now ignored, the process is shown to be relevant, especially for the correct estimate of swell. Following the practical impossibility of devoted field experiments, we exploit the global model results over a period of more than four years to extract the tiny signal associated to the attenuation by rain. A direct comparison of the ratio model by altimeter significant wave heights versus the encountered rain amount hints to a marked related dependence. A proper quantification of the related physical effect requires a multiple step procedure that we describe in detail. We check the reliability of the results, and we provide the related source function ready for implementation in operational wave models.
SOSPES: SPIRIVA® observational study measuring SGRQ score in routine medical practice in Central and Eastern Europe

Purpose The long-acting inhaled anticholinergic agent, tiotropium, is recommended as first-line maintenance therapy for moderate to very severe Chronic Obstructive Pulmonary Disease (COPD) to improve symptoms, exercise tolerance, health status, and to reduce exacerbations. Few studies have evaluated the therapeutic efficacy of tiotropium in patients in routine clinical conditions. The current study was designed to investigate the therapeutic efficacy of tiotropium delivered via the HandiHaler® device on the health status of patients with COPD with Global initiative for chronic Obstructive Lung Disease (GOLD) disease classification 2–4 in six central and eastern European countries in a real-life clinical setting. Methods The study was an open-label, prospective, uncontrolled, and single-arm surveillance study with three clinic visits during a 6-month observation period (baseline, and months 3 and 6). Health status was measured using the disease-specific St George’s Respiratory Questionnaire (SGRQ). The primary efficacy endpoint was the mean change from baseline in SGRQ total score at the end of the 6-month observational period. Results Patients treated with tiotropium 18 μg once daily showed statistically significant and clinically meaningful reduction (improvement) of 21.7 units in the SGRQ total score, regardless of smoking status or cardiac comorbidities at enrollment (P < 0.0001). The analysis also showed that age, treatment compliance, and GOLD disease classification were significant factors that impact the health status of patients with COPD differently. Conclusion These results provide further support for the use of the tiotropium HandiHaler® as first-line maintenance treatment of patients with COPD with a clinician-assessed disease.
Pathophysiology of Cerebral Small Vessels in Vascular Cognitive Impairment

Cerebral small-vessel alterations play a central role in determining lesions of subcortical structures and eventually may lead to cognitive impairment. Small-vessel diseases are classified according to the pathological viewpoint. The most important ones are the changes in small arteries and arterioles caused by prolonged hypertension. These small-vessel changes may result in ischemic damage to the brain parenchyma and blood-barrier alterations. Both mechanisms are thought to contribute to the occurrence of white-matter changes and lacunar infarcts. Modern magnetic resonance techniques such as diffusion, perfusion, and spectroscopy may allow the in vivo study of the pathophysiology of small-vessel diseases and the consequences on the brain parenchyma.
Diagnostic accuracy of self collected vaginal specimens for human papillomavirus compared to clinician collected human papillomavirus specimens: a meta-analysis

Background/objectives: Providing summary recommendations regarding self collection of vaginal specimens for human papillomavirus (HPV) testing is difficult owing to the wide range of published estimates for the diagnostic accuracy of this approach. To determine summary estimates from analyses of reported findings of the sensitivity, specificity and summary receiver operating characteristic curves (SROC) for self collected vaginal specimens for HPV testing compared to the reference standard, clinician collected HPV specimens. Methods: Standard search criteria for a diagnostic systematic review were employed. Eligible studies were combined using a random effects model and summary ROC curves were derived for overall and for specific subgroups. Results: Summary measures were determined from 12 studies. Six studies where patients used Dacron or cotton swabs or cytobrushes to obtain samples were pooled and had an overall sensitivity of 0.74 (95% CI 0.61 to 0.84) and specificity of 0.88 (95% CI 0.83 to 0.92), with diagnostic odds ratio of 22.3 and an area under the curve of 0.91. Self specimens using Dacron or cotton swabs or cytobrushes collected by women enrolled at referral clinics had an overall sensitivity of 0.81 (95% CI 0.65 to 0.91) and specificity of 0.90 (95% CI 0.80 to 0.95). Sensitivity and specificity of tampons ranged from 0.67–0.94 and 0.80–0.85 respectively. Conclusions: Our findings indicate that the combined sensitivity for HPV-DNA is more than 70% when patients use Dacron swabs, cotton swabs, or cytobrushes to obtain their own vaginal specimens for HPV-DNA evaluation. Self collected HPV-DNA swabs may be an appropriate alternative for low resource settings or in patients reluctant to undergo pelvic examinations.
Bayesian Analysis of Lidar Signals with Multiple Returns

Time-correlated single photon counting and burst illumination laser data can be used for range profiling and target classification. In general, the problem is to analyze the response from a histogram of either photon counts or integrated intensities to assess the number, positions, and amplitudes of the reflected returns from object surfaces. The goal of our work is a complete characterization of the 3D surfaces viewed by the laser imaging system. The authors present a unified theory of pixel processing that is applicable to both approaches based on a Bayesian framework, which allows for careful and thorough treatment of all types of uncertainties associated with the data. We use reversible jump Markov chain Monte Carlo (RJMCMC) techniques to evaluate the posterior distribution of the parameters and to explore spaces with different dimensionality. Further, we use a delayed rejection step to allow the generated Markov chain to mix better through the use of different proposal distributions. The approach is demonstrated on simulated and real data, showing that the return parameters can be estimated to a high degree of accuracy. We also show some practical examples from both near and far-range depth imaging.
Complex object motion represented by context‐dependent correlated activity of visual interneurones

Accurate and adaptive encoding of complex, dynamic visual information is critical for the survival of many animals. Studies across a range of taxa have investigated behavioral and neuronal responses to objects that represent a threat, such as a looming object approaching along a direct collision course. By investigating neural mechanisms of avoidance behaviors through recording multineuronal activity, it is possible to better understand how complex visual information is represented in circuits that ultimately drive behaviors. We used multichannel electrodes to record from the well‐studied locust nervous system to explore how object motion is reflected in activity of correlated neural activity. We presented locusts (Locusta migratoria) with objects that moved along one of 11 unique trajectories and recorded from descending interneurons within the ventral nerve cord. Spike sorting resulted in 405 discriminated units across 20 locusts and we found that 75% of the units responded to some form of object motion. Dimensionality reduction through principal component (PCA) and dynamic factor (DFA) analyses revealed population vector responses within individuals and common firing trends across the pool of discriminated units, respectively. Population vector composition (PCA) varied with the stimulus and common trends (DFA) showed unique tuning related to changes in the visual size and trajectory of the object through time. These findings demonstrate that this well‐described collision detection system is more complex than previously envisioned and will drive future experiments to explore fundamental principles of how visual information is processed through context‐dependent dynamic ensembles of neurons to initiate and control complex behavior.