Miracle-dz/UniFAR-FTUs huggingface dataset:
The claustrum of the sheep and its connections to the visual cortex

The present study analyses the organization and selected neurochemical features of the claustrum and visual cortex of the sheep, based on the patterns of calcium‐binding proteins expression. Connections of the claustrum with the visual cortex have been studied by tractography. Parvalbumin‐immunoreactive (PV‐ir) and Calbindin‐immunoreactive (CB‐ir) cell bodies increased along the rostro‐caudal axis of the nucleus. Calretinin (CR)‐labeled somata were few and evenly distributed along the rostro‐caudal axis. PV and CB distribution in the visual cortex was characterized by larger round and multipolar cells for PV, and more bitufted neurons for CB. The staining pattern for PV was the opposite of that of CR, which showed densely stained but rare cell bodies.
Stratum corneum lipidomics analysis reveals altered ceramide profile in atopic dermatitis patients across body sites with correlated changes in skin microbiome

Atopic dermatitis (AD) is driven by the interplay between a dysfunctional epidermal barrier and a skewed cutaneous immune dysregulation. As part of the complex skin barrier dysfunction, abnormalities in lipid organization and microbiome composition have been described. We set out to systematically investigate the composition of the stratum corneum lipidome, skin microbiome and skin physiology parameters at three different body sites in patients with AD and healthy volunteers.
Impact of Tumor-Infiltrating Lymphocytes on Overall Survival in Merkel Cell Carcinoma.

BACKGROUND Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine carcinoma of the skin. As the clinical course can be variable, prognostic markers are needed to better stratify patients. Prior literature, composed of small series with limited sample size, has demonstrated that tumor-infiltrating lymphocytes (TILs) are an important prognostic marker in MCC. To validate these findings on a population level, we sought to analyze and report the prognostic value of TILs in a large national data set. MATERIALS AND METHODS A retrospective observational cohort study was conducted of patients with nonmetastatic MCC from 2010 to 2015 using the National Cancer Database. Individual variables trending toward significance using a univariable analysis were included in a multivariable Cox proportional hazards model to assess their independent effect on overall survival (OS). TILs were subclassified into none, nonbrisk, and brisk and the survival analysis was performed. Propensity score-weighted multivariable analysis (PS MVA) was performed to adjust for additional confounding. RESULTS A total of 2,182 patients met inclusion criteria: 611 (28.0%) were identified as having TILs present, and 1,571 (72.0%) had TILs absent in the tumor. On MVA, subdivision of TIL status into nonbrisk (hazard ratio [HR], 0.750; 95% confidence interval [CI], 0.602-0.933) and brisk (HR, 0.499; 95% CI, 0.338-0.735) was associated with incrementally improved OS compared with no TILs. The association of nonbrisk and brisk TILs with improved OS was retained on PS MVA (Nonbrisk: HR, 0.720; 95% CI, 0.550-0.944; Brisk: HR, 0.483; 95% CI, 0.286-0.814). CONCLUSION The presence of nonbrisk and brisk TILs is associated with incrementally improved OS in patients with nonmetastatic MCC in a large national data set. This pathologic feature can aid with risk stratification, estimation of prognosis, and, importantly, decision-making with respect to treatment intensification in high-risk patients. IMPLICATIONS FOR PRACTICE Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine carcinoma of the skin with variable clinical course. Prognostic markers are thus needed to better stratify patients at presentation. This analysis represents the largest retrospective observational cohort study of patients with nonmetastatic MCC using the National Cancer Database. It demonstrates that increasing degrees of tumor infiltration by lymphocytes (nonbrisk and brisk, respectively) are associated with incrementally improved survival. This manuscript will impact modern practice by improving our understanding of pathologic findings that aid with risk stratification, estimation of prognosis, and, importantly, decision-making with respect to treatment intensification in high-risk patients. Intensification may include offering adjuvant radiation therapy to the primary site after wide excision despite small (<1 cm) tumor size, to the nodal basin in sentinel lymph node-negative patients, or offering closer follow-up with routine imaging to rule out recurrent or metastatic disease.
3D car-detection based on a Mobile Deep Sensor Fusion Model and real-scene applications

Unmanned vehicles need to make a comprehensive perception of the surrounding environmental information during driving. Perception of automotive information is of significance. In the field of automotive perception, the sterevision of car-detection plays a vital role and sterevision can calculate the length, width, and height of a car, making the car more specific. However, under the existing technology, it is impossible to obtain accurate detection in a complex environment by relying on a single sensor. Therefore, it is particularly important to study the complex sensing technology based on multi-sensor fusion. Recently, with the development of deep learning in the field of vision, a mobile sensor-fusion method based on deep learning is proposed and applied in this paper——Mobile Deep Sensor Fusion Model (MDSFM). The content of this article is as follows. It does a data processing that projects 3D data to 2D data, which can form a dataset suitable for the model, thereby training data more efficiently. In the modules of LiDAR, it uses a revised squeezeNet structure to lighten the model and reduce parameters. In the modules of cameras, it uses the improved design of detecting module in R-CNN with a Mobile Spatial Attention Module (MSAM). In the fused part, it uses a dual-view deep fusing structure. And then it selects images from the KITTI’s datasets for validation to test this model. Compared with other recognized methods, it shows that our model has a fairly good performance. Finally, it implements a ROS program on the experimental car and our model is in good condition. The result shows that it can improve performance of detecting easy cars significantly through MDSFM. It increases the quality of the detected data and improves the generalized ability of car-detection model. It improves contextual relevance and preserves background information. It remains stable in driverless environments. It is applied in the realistic scenario and proves that the model has a good practical value.
Compete or Coexist? Why the Same Mechanisms of Symmetry Breaking Can Yield Distinct Outcomes

Cellular morphogenesis is governed by the prepattern based on the symmetry-breaking emergence of dense protein clusters. Thus, a cluster of active GTPase Cdc42 marks the site of nascent bud in the baker’s yeast. An important biological question is which mechanisms control the number of pattern maxima (spots) and, thus, the number of nascent cellular structures. Distinct flavors of theoretical models seem to suggest different predictions. While the classical Turing scenario leads to an array of stably coexisting multiple structures, mass-conserved models predict formation of a single spot that emerges via the greedy competition between the pattern maxima for the common molecular resources. Both the outcome and the kinetics of this competition are of significant biological importance but remained poorly explored. Recent theoretical analyses largely addressed these questions, but their results have not yet been fully appreciated by the broad biological community. Keeping mathematical apparatus and jargon to the minimum, we review the main conclusions of these analyses with their biological implications in mind. Focusing on the specific example of pattern formation by small GTPases, we speculate on the features of the patterning mechanisms that bypass competition and favor formation of multiple coexisting structures and contrast them with those of the mechanisms that harness competition to form unique cellular structures.
The Nubeam reference-free approach to analyze metagenomic sequencing reads

We present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and assigns numbers to reads based on the product matrix. Nubeam capitalizes on the noncommutative property of matrix multiplication, such that different reads are assigned different numbers and similar reads similar numbers. A sample, which is a collection of reads, becomes a collection of numbers that form an empirical distribution. We demonstrate that the genetic difference between samples can be quantified by the distance between empirical distributions. Nubeam includes the k-mer method as a special case, but unlike the k-mer method, it is convenient for Nubeam to account for GC bias and nucleotide quality. As a reference-free approach, Nubeam avoids reference bias and mapping bias, and can work with organisms without reference genomes. Thus, Nubeam is ideal to analyze data sets from metagenomics whole genome shotgun (WGS) sequencing, where the amount of unmapped reads is substantial. When applied to a WGS sequencing data set to quantify distances between metagenomics samples from various human body habitats, Nubeam recapitulates findings made by mapping-based methods and sheds light on contributions of unmapped reads. Nubeam is also useful in analyzing 16S rRNA sequencing data, which is a more prevalent type of data set in metagenomics studies. In our analysis, Nubeam recapitulated the findings that natural microbiota in mouse gut are resilient under challenges, and Nubeam detected differences in vaginal microbiota between cases of polycystic ovary syndrome and healthy controls.
A Kink in the Line: Does a Unique Lateral-Line Peculiarity Really Characterize Lake Malaŵi's Huge Haplochromine Species Flock (Teleostei: Cichlidae)?

Abstract A downward kink one or more scales in length at the posterior end of the upper lateral line, leaving only one scale row instead of two between it and the lower lateral line, has been considered a synapomorphy uniting as a monophyletic group all members of both clades of endemic haplochromine cichlids of Lake Malaŵi. Here, this claim is tested by surveying the character in representatives of all genera of Lake Malaŵi haplochromines (tribe Haplochromini of the subfamily Pseudocrenilabrinae). Presence of the kink is shown to be variable in most genera, and it was not documented at all in two (Abactochromis, Cyrtocara). Specimens with no kink occur in many genera, and kink presence and length frequently vary on the two sides of the body. Thus, it is difficult to justify the kink as a synapomorphy of the species flock. The two clades differ in kink frequency; a kink occurred on at least one side of the body in 79% of bilaterally assessable specimens in the non-mbuna clade, but in only 53% of those in the mbuna clade (p < 0.0001). When a kink is present, its length is more variable in non-mbuna (1 to 8 scales, mode 2) than mbuna (1 to 4 scales, mode 1). Extension of the upper lateral line backward from the upper flank close to or onto the caudal peduncle, where no scale row is as dorsally situated, is identified as one cause of kink existence; additional factors likely await discovery. Contrary to published statements, the kink is expressed in some specimens of Astatotilapia calliptera, a phylogenetically important nonendemic haplochromine found in Lake Malaŵi and elsewhere, which may be the sister of the lake's endemic flock. An apparently identical lateral-line kink occurs sporadically in haplochromines in other lakes and in members of three other pseudocrenilabrine cichlid tribes, further refuting the hypothesis that this character is a synapomorphy of the Lake Malaŵi species flock.
Novel perspectives on stomatal impressions: Rapid and non-invasive surface characterization of plant leaves by scanning electron microscopy

Scanning electron microscopy (SEM) is widely used to investigate the surface morphology, and physiological state of plant leaves. Conventionally used methods for sample preparation are invasive, irreversible, require skill and expensive equipment, and are time and labor consuming. This study demonstrates a method to obtain in vivo surface information of plant leaves by imaging replicas with SEM that is rapid and non-invasive. Dental putty was applied to the leaves for 5 minutes and then removed. Replicas were then imaged with SEM and compared to fresh leaves, and leaves that were processed conventionally by chemical fixation, dehydration and critical point drying. The surface structure of leaves was well preserved on the replicas. The outline of epidermal as well as guard cells could be clearly distinguished enabling determination of stomatal density. Comparison of the dimensions of guard cells revealed that replicas did not differ from fresh leaves, while conventional sample preparation induced strong shrinkage (-40% in length and -38% in width) of the cells when compared to guard cells on fresh leaves. Tilting the replicas enabled clear measurement of stomatal aperture dimensions. Summing up, the major advantages of this method are that it is inexpensive, non-toxic, simple to apply, can be performed in the field, and that results on stomatal density and in vivo stomatal dimensions in 3D can be obtained in a few minutes.
Reintroduction of tocilizumab elicited macrophage activation syndrome in a patient with adult-onset Still’s disease with a previous successful tocilizumab treatment

Abstract Macrophage activation syndrome (MAS) is a form of secondary hemophagocytic lymphohistiocytosis and is a rapidly progressive, life-threatening complication of adult-onset Still’s disease (AOSD). An anti-IL-6 receptor monoclonal antibody, tocilizumab, has shown to be effective in the treatment of AOSD but may precipitate MAS in patients with AOSD. The precise mechanism of MAS developed during anti-cytokine biologic agents remains unknown, but selective inhibition of a subset of pathways could impact other immune signalling pathways and trigger MAS. We herein describe a case of AOSD with the opposite outcomes of tocilizumab therapy, remission and development of MAS, after tocilizumab treatment at the initial flare and the relapse. From the comparison of clinical characteristics and concomitant treatment around the time of starting tocilizumab in both flares, the type and intensity of concomitant immunosuppressive therapy might strongly affect MAS development during tocilizumab therapy.
Clinical efficiency and safety of the oticon medical neuro cochlear implant system: a multicenter prospective longitudinal study

ABSTRACT Objective This prospective longitudinal cohort study at six tertiary referral centers in Canada and Denmark describes the clinical efficiency and surgical safety of cochlear implantation with the Oticon Medical Neuro cochlear implant system, including the Neuro Zti implant, the EVO electrode array, and the Neuro One sound processor. Methods Patients were adult cochlear implant candidates with bilateral sensorineural hearing loss. Results The mean HINT scores in quiet pre-operatively and at 3, 6, and 12 months post-activation were 13%, 58%, 67%, and 72%, respectively, and in noise (+10 dB SNR) 13%, 46%, 53%, and 59%, respectively. The mean improvement from baseline to 6 months post-activation was 54% in quiet and 40% in noise. The surgical major complication incidence rate was 0% and the post-surgical major complication incidence rate (until 12 months post-activation) was 4%. There was no adverse event that was fatal, that required explantation, or that resulted in sound processor nonuse, and no implant failure. Conclusion Cochlear implantation with the Oticon Medical Neuro system enables speech identification both in quiet and in noise and audiologic outcomes continue to improve in the year following activation. No substantial adverse events occurred during the surgical implantation procedure and during the 12 months post-activation.
Impact of dynamic greenspace exposure on symptomatology in individuals with schizophrenia

There are currently many tools available for capturing and defining the context of one’s environment. Digital phenotyping, the use of technology and sensors to capture moment-to-moment behavior, has shown potential in quantifying the lived experience of mental illness and in the identification of individualized targets related to recovery. Environmental data suggests that greenspace may have a restorative capacity on mental health. In this paper, we explore the relationship of greenspace derived from geolocation with self-reported symptomatology from individuals with schizophrenia as well as healthy controls. Individuals with schizophrenia had less exposure to greenspace than controls, but their exposure demonstrated a dosage effect: high greenspace environments were associated with lower symptoms for anxiety (Cohen’s d = -0.70), depression (d = -0.97), and psychosis (d = -0.94), whereas effect sizes for healthy controls were all negligible or small (d < 0.38). The notion that greenspace may have a more pronounced effect on individuals with mental illness presents both potential areas for recovery as well as implications for health care policy, especially in cities with a broad range of greenspace environments.
Poly-Victimization Among Female College Students: Are the Risk Factors the Same as Those Who Experience One Type of Victimization?

Past research has shown that a significant proportion of college students will experience a victimization during their college tenure. This body of research provides evidence that college students’ lifestyle characteristics and routine activities play a role in influencing their risk of victimization; yet, little is known about whether these same risk factors predict both single-type victimization and poly-victimization. Using a sample of more than 4,000 college women from across the United States, multivariate analyses were used to examine the risk factors for poly-victimization. Measures from both target congruence theory and lifestyles-routine activities theory were found to significantly differentiate single-type victims from poly-victims.
Insights into Disease-Associated Tau Impact on Mitochondria

Abnormal tau protein aggregation in the brain is a hallmark of tauopathies, such as frontotemporal lobar degeneration and Alzheimer’s disease. Substantial evidence has been linking tau to neurodegeneration, but the underlying mechanisms have yet to be clearly identified. Mitochondria are paramount organelles in neurons, as they provide the main source of energy (adenosine triphosphate) to these highly energetic cells. Mitochondrial dysfunction was identified as an early event of neurodegenerative diseases occurring even before the cognitive deficits. Tau protein was shown to interact with mitochondrial proteins and to impair mitochondrial bioenergetics and dynamics, leading to neurotoxicity. In this review, we discuss in detail the different impacts of disease-associated tau protein on mitochondrial functions, including mitochondrial transport, network dynamics, mitophagy and bioenergetics. We also give new insights about the effects of abnormal tau protein on mitochondrial neurosteroidogenesis, as well as on the endoplasmic reticulum-mitochondria coupling. A better understanding of the pathomechanisms of abnormal tau-induced mitochondrial failure may help to identify new targets for therapeutic interventions.
The Effects of Progressive Relaxation Exercises following Lumbar Surgery: A Randomized Controlled Trial

Background and Aim: This study aimed to examine the effect of progressive relaxation exercises on anxiety, pain, and sleep quality among patients who underwent surgery for lumbar disc hernia. Materials and Methods: This randomized, non-blinded, parallel-group clinical trial was conducted with 97 patients who had a lumbar microdiscectomy. On the first, second, and third day of the postoperative period, routine nursing care was performed on the control group, while additional progressive relation exercises were performed on the experimental group. Results: When the experimental and control groups were compared regarding SAI, VAS-P, and VAS-S scores before the surgery, no differences were found (p > 0.05); however, there were significant differences in the scores obtained on the mornings of the second and third days after the surgery (p < 0.05). Conclusions: Progressive relation exercises used as a supportive nursing intervention were found to reduce pain and anxiety and increase sleep quality.
Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry

Stoichiometry of nucleotide binding to AAA+ ATPase PAN was established using native MS. Utilization of a Walker A mutant PANKA, which is impaired in nucleotide binding as an internal standard minimized the impact of residual solvation on mass measurement accuracy. PAN hexamer dissociation products and over-charged species – both maintaining nucleotide binding – were observed at highly variable levels. We hypothesize that these phenomena originated at the final stages of ESI droplet evolution, their extent dependent on minute changes in emitter performance. Graphical Abstract Highlights All six binding sites in PANWT are occupied by ADP- or ATP-type nucleotides. PANKA Walker A mutant substoichiometrically binds ATP- but not ADP-type nucleotides. PAN hexamer dissociation of the solution origin characteristics was observed in MS. We posit that the PAN hexamer dissociation proceeds within the ESI droplets. AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) 6-fold symmetry. In a subset of AAA+ ATPases that facilitate protein unfolding and degradation, six subunits cooperate to translocate protein substrates through a central pore in the ring. The number and type of nucleotides in an AAA+ ATPase hexamer is inherently linked to the mechanism that underlies cooperation among subunits and couples ATP hydrolysis with substrate translocation. We conducted a native MS study of a monodispersed form of PAN, an archaeal proteasome AAA+ ATPase, to determine the number of nucleotides bound to each hexamer of the WT protein. We utilized ADP and its analogs (TNP-ADP and mant-ADP), and a nonhydrolyzable ATP analog (AMP-PNP) to study nucleotide site occupancy within the PAN hexamer in ADP- and ATP-binding states, respectively. Throughout all experiments we used a Walker A mutant (PANK217A) that is impaired in nucleotide binding as an internal standard to mitigate the effects of residual solvation on mass measurement accuracy and to serve as a reference protein to control for nonspecific nucleotide binding. This approach led to the unambiguous finding that a WT PAN hexamer carried – from expression host – six tightly bound ADP molecules that could be exchanged for ADP and ATP analogs. Although the Walker A mutant did not bind ADP analogs, it did bind AMP-PNP, albeit at multiple stoichiometries. We observed variable levels of hexamer dissociation and an appearance of multimeric species with the over-charged molecular ion distributions across repeated experiments. We posit that these phenomena originated during ESI process at the final stages of ESI droplet evolution.