Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitosis in the intact and regenerating planarian Dugesia mediterranea n.sp. II. Mitotic studies during regeneration, and a possible mechanism of blastema formation

In planarian regeneration mitosis occurs in both anterior and posterior blastemas. The mitotic increase is visible as early as one hour after amputation, reaches a rapid first maximum at 5–12 hours, a relative minimum at 24–30 hours, and a higher and longer second maximum at two to four days depending on body size, level of amputation, and on whether blastema is anterior or posterior. The spatial dynamics of mitosis show a rapid and high mitotic increase in the distal regions but not in the proximal regions. Later, the proliferative zone shifts in sucessive mitotic waves to more proximal regions, paralleling the formation of the head ganglia and nerve cords. These results do not agree with theories of blastema formation through neoblast migration or through cell dedifferentiation, in as much as the local proliferation of neoblasts encountered is sufficiently high and early to account for the number of blastema cells found during period of regeneration. Therefore, we suggest that blastema formation during planarian regeneration occurs mainly through local neoblast proliferation. These results and the data obtained on regeneration rates enable us to suggest that nervous tissue may be one of the factors responsible for the differing mitotic increases found. Since neoblasts are the only planarian cells capable of mitosis, we suggest that neoblast proliferation could be under nervous tissue control through some stimulatory substance (s) released from the nerve terminals. The implications of this hypothesis for the maintenance of axial polarity are also discussed.
Electroacupuncture ameliorates corticotrophin-releasing factor-induced jejunal dysmotility in a rat model of stress

Background Central injection of corticotrophin-releasing factor (CRF) mimics the effect of stress on gastrointestinal (GI) responses, including inhibition of GI motility. This study was designed to explore the effects of electroacupuncture (EA) on disordered jejunal motility in a rat model of stress induced by intracisternal (IC) injection of CRF. Methods A stress model was established by IC injection of CRF in Sprague–Dawley rats. GI motility was evaluated by assessing gastric emptying (GE), gastrointestinal transit (GIT) and jejunal motility in vivo. EA was performed at ST36. The functional roles of CRF receptor subtype 1 and subtype 2 (CRFr1 and CRFr2) were examined by IC administration of the corresponding selective CRF antagonists. Protein expression of CRFr1 and CRFr2 in the hypothalamus and jejunum was detected by Western blotting. Results IC injection of CRF significantly inhibited GE, GIT and jejunal motility. EA treatment remarkably improved the disturbed GI motility. Intriguingly, the disordered jejunal motility induced by central CRF was abolished by IC injection of a selective CRFr2 antagonist, indicating the essential role of central CRFr2 in mediating the stress-induced jejunal motor disorder. EA at ST36 decreased central and peripheral expression of CRFr2, which might be one of the potential mechanisms underlying the beneficial effect of EA on jejunal dysmotility in this rat model of stress. Conclusion This study suggested that EA at ST36 could ameliorate disordered jejunal motility induced by stress, and that this might be associated with the down-regulation of CRFr2.
Role Incongruence and Psychological Stress Symptoms in Substitute Decision Makers of Intensive Care Patients.

BACKGROUND Most intensive care patients require substitute decision makers (SDMs) to make decisions. The SDMs may prefer an active, shared, or passive decision-making role. Role incongruence is when preferred and actual roles differ. OBJECTIVE To evaluate the impact of decision-making role preferences and role incongruence on psychological distress symptoms in SDMs. METHODS A multicenter, interviewer-administered survey was conducted among SDMs of critically ill adults. The Control Preferences Scale was used to evaluate role preferences. Psychological distress was defined as anxiety, depression, or posttraumatic stress symptoms with predefined cut points on the Hospital Anxiety and Depression Scale (score > 10 on the anxiety or the depression subscale) and Impact of Events Scale (score > 30). RESULTS One hundred eighty SDMs were recruited; 64% responded. Most were white (71%) and female (65%); 46% were spouses. Role preferences varied: active, 24%; shared, 44%; and passive, 31%. Almost half (49%) reported incongruence. Symptom prevalence was 50% for posttraumatic stress, 32% for anxiety, and 16% for depression. Most (56%) reported some psychological distress. In multivariable logistic regression, the composite outcome of psychological distress was independently associated with patient death (odds ratio, 2.95; 95% CI, 1.08-8.02; P = .03), female sex of SDM (odds ratio, 2.96; 95% CI, 1.49-5.89; P = .002), and incongruence (odds ratio, 3.26; 95% CI, 1.67-6.36; P < .001). CONCLUSIONS Adverse psychological symptoms are prevalent in SDMs of critically ill patients and are related to role incongruence.
A Bibliometric Review of Artificial Extracellular Matrices Based on Tissue Engineering Technology Literature: 1990 through 2019

Artificial extracellular matrices (aECMs) are an extension of biomaterials that were developed as in-vitro model environments for tissue cells that mimic the native in vivo target tissues’ structure. This bibliometric analysis evaluated the research productivity regarding aECM based on tissue engineering technology. The Web of Science citation index was examined for articles published from 1990 through 2019 using three distinct aECM-related topic sets. Data were also visualized using network analyses (VOSviewer). Terms related to in-vitro, scaffolds, collagen, hydrogels, and differentiation were reoccurring in the aECM-related literature over time. Publications with terms related to a clinical direction (wound healing, stem cells, artificial skin, in-vivo, and bone regeneration) have steadily increased, as have the number of countries and institutions involved in the artificial extracellular matrix. As progress with 3D scaffolds continues to advance, it will become the most promising technology to provide a therapeutic option to repair or replace damaged tissue.
Female Red-Breasted Flycatchers (Ficedula Parva) mated with older males produce male-biased broods

ABSTRACT Recent avian studies suggest that offspring sex ratios can vary with environmental or parental characteristics. One example is that females may adjust brood sex ratio of fledglings in response to the sexual attractiveness of their mate and are expected to produce more sons when mated with older or more ornamented males. We determined offspring sex ratios at fledging (158 nestlings from 33 broods) in a population of migratory bird species, Red-breasted Flycatchers (Ficedula parva) that were breeding on the western edge of their geographic range, in the strictly protected part of the Białowieża Forest (north-eastern Poland). The ratio of individual broods ranged from all male to all female, but the average offspring sex ratio at the population level did not deviate significantly from the expected 50:50 sex ratio. Moreover, we found no evidence that sex ratio varied significantly with year, with the incidence of extra-pair paternity, with partial brood losses, or with brood size. However, females mated to older males (older males are also more ornamented) were significantly more likely to produce male-biased broods. Our data suggest that female Red-breasted Flycatchers manipulate sex ratio in response to their mate’s age.
Efficacy and Safety of Botulinum Toxin Type A in Preventing Postoperative Scars and Improving the Cosmetic Appearance of Scars: A Systematic Review and Meta-Analysis

Background Scars with poor cosmesis that develop after wound healing may affect normal life. Objective To assess the efficacy and safety of botulinum toxin type A (BTXA) in preventing postoperative hypertrophic scars or keloids. Methods A systematic review was performed by searching the PubMed, Cochrane Library, and EMBASE databases from their inception date up to February 2020 for randomized controlled trials (RCTs) evaluating the efficacy of BTXA in preventing hypertrophic scars or keloids. The primary outcome measures included the Vancouver Scar Scale (VSS) score, Visual Analog Scale (VAS) score, scar width, patient satisfaction, and adverse events. Results Twelve RCTs involving 497 cases (372 patients) were included. The meta-analysis showed significant differences in the VAS score (weighted mean difference [WMD] = 1.31, 95% CI = 1.06 to 1.55, P < .00001), VSS score (WMD = −1.02, 95% CI = −1.72 to −0.32, P = .004), scar width (WMD = −0.18, 95% CI = −0.29 to −0.08, P = .0008), and patient satisfaction (relative risk = 1.25, 95% CI = 1.06-1.49, P = .01). Four studies reported trivial adverse events. Conclusions This meta-analysis showed that BTXA was more effective than the control treatment in preventing postoperative scars and improving the cosmetic appearance of facial scars for East Asians, and no serious adverse events were found during the follow-up period. However, there was insufficient evidence to support the use of BTXA for the prevention of scars in patients from other ethnic groups and regions or scars in non-facial areas.
Corrections

DEVELOPMENTAL BIOLOGY Correction for “The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: Analysis of ESTs from the hermaphroditic strain,” by Ricardo M. Zayas, Alvaro Hernández, Bianca Habermann, Yuying Wang, Joel M. Stary, and Phillip A. Newmark, which appeared in issue 51, December 20, 2005, of Proc Natl Acad Sci USA (102:18491–18496; first published December 12, 2005; 10.1073/pnas.0509507102). The authors note that on page 18496, left column, the first full paragraph appeared incorrectly. This paragraph should instead appear as the following: For in situ analysis, we also chose additional candidate genes implicated in reproductive processes based on BLASTX similarity; these genes were not annotated to the GO term “reproduction. ” For example, we studied planarian homologues of cdc-5/polo-like kinases, important regulators of cell cycle checkpoints (54) also implicated in the coordination of chromosome segregation during meiosis (55); the mammalian sperm tail protein, Shippo-1 (56); and spermatid elongation defective 1 (sped-1), a gene required for proper spermatid elongation. All of these genes were expressed in the planarian testes. A planarian homologue of gld-1, a gene required for oocyte development in C. elegans (58), was detected in the ovaries and oviducts (Fig. 4A). The expression of sped-1-like mRNA was used to monitor the development of the testes (Fig. 4B). sped-1-like mRNA was not detected in 2to 3-day-old hatchlings; the transcript was first detectable in the testes primordia of juvenile planarians and strongly expressed in the testes of mature worms (Fig. 4B). sped-1-like mRNA was not detected in asexual worms; consistent with this observation, Northern blot analysis showed that this gene is expressed at high levels in sexual worms but is undetectable in asexual animals (data not shown). These results provide additional evidence that the planarian reproductive organs are formed postembryonically (5, 8–11, 14). In addition, Fig. 4 and its legend appeared incorrectly. The corrected figure and its legend appear below.
An Experimental Approach to the Reclamation of a Limestone Quarry Floor: The First Three Years

‘Three-inch [7.5 cm] crusher-run’ limestone proved entirely suitable as a substratum for the rapid establishment of pioneer vegetation on a quarry floor, but only with the addition of fertilizers. A manure derived from sewage and an NPK fertilizer mixture proved suitable additives. A grass variety (Festuca rubra var. fallax Hack.) was sown, and became established on the substratum treated with either additive. Immigrant mosses soon became dominant in a grass/moss community on the manured substratum, whilst F. rubra retained its ascendancy on the NPK-treated material. The moss-dominated community was not attractive to Rabbits, whereas the grass-dominated community proved attractive to these animals which are accepted as beneficial for conservation in this particular context. Further observations are required to assess (a) whether the by-passing of a cryptogamic stage in the prisere encouraged by the NPK mixture is a worthwhile objective, (b) whether the observed dominance of mosses encouraged by manure will be broken by F. rubra, and (c) whether the establishment of desirable immigrant species occurs differentially between the treatments. Meanwhile a perceptible degree of rehabilitation within three years may be claimed as a result of treatments producing a total plant cover of between 40% and 70%.
Crystal structure of TEX101, a glycoprotein essential for male fertility, reveals the presence of tandemly arranged Ly6/uPAR domains

Testis‐expressed gene 101 (TEX101) is a glycosyl‐phosphatidylinositol‐anchored glycoprotein essential for sperm fertility and spermatogenesis. TEX101 interacts with lymphocyte antigen 6 complex, locus K (Ly6k) as well as a disintegrin and metallopeptidase domain 3 (ADAM3). Although these proteins are considered essential for fertility, the associated mechanisms remain uncharacterized. Herein, we determined the crystal structure of human and mouse TEX101, revealing that TEX101 contains two tandem Ly6/uPAR (LU) domains. Detailed structural analyses revealed characteristic surfaces of TEX101 that may be involved in the interactions with other proteins or membranes. These results provide the structural basis for the role of TEX101 in fertilization and could contribute to developing diagnostic methods and treatments for infertility or developing male contraceptives.
Clinical Wisdom

A diversity of cultural, economic and social factors influence our professional work as psychotherapists, and hardly anything we do with our patients is not dependent upon society’s political and moral choices. Moreover, what can be regarded as wisdom is difficult to agree upon, more so for group analysts. It must be felt wise, maybe more easily seen at a distance, and best found by asking men or women, in whom we trust. This article will explore fundamental ideas and assumptions regarding the art of helping patients by psychotherapy. The focus is on group analytic psychotherapy and the use of it in psychiatry. Some of the questions are: What shall be modified in the method and technique to make it helpful to the patients, and will it be possible to meet the requirements of validation from the public health services? Can research and the researcher be of use in group analysis and do we at all have a mutual case? Clinical knowledge from psychotherapy research and retrieved reflections from wise colleagues, on what can be regarded the most essential experiences in therapeutic groups, are presented. Emphasis will be on the therapist’s personal development and existential challenges. Shakespeare’s tale about ‘the choice of the three caskets’ illustrates some moral choices, which can also be regarded as choices for the therapist.
Induction of epigenetic reprogramming in fibroblast by extracts of carcinoma

Recently, differentiated somatic cells had been reprogrammed to pluripotential state in vitro, and various tissue cells had been elicited from those cells. Epigenetic modifications allow differentiated cells to perpetuate the molecular memory to retain their identity. In this study, NIH/3T3 fibroblasts were dedifferentiated with F9 cellular extract, and were detected using the gene expression pattern and the DNA methylation level in the dedifferentiated cells. The expression of embryonic marker Sox2, klf4, c-Myc and Oct4 were analyzed by real-time polymerase chain reaction (RT-PCR), and the total levels of cellular DNA methylation in dedifferentiated NIH/3T3 fibroblasts were measured by flow cytometry. According to the results, Sox2, klf4, c-Myc and Oct4 were expressed in NIH/3T3 fibroblasts after F9 cellular extract co-incubation. Also, the total DNA methylation level significantly decreased after the treatment. The data indicated that the extract of F9 cells can dedifferentiate NIH/3T3 cells, and make modified NIH/3T3 cells express transcription factors associated with totipotent and pluripotent cells. Key words: Fibroblasts, reprogramming, methylation, epigenesis, carcinoma.
Deep Learning for Multigrade Brain Tumor Classification in Smart Healthcare Systems: A Prospective Survey

Brain tumor is one of the most dangerous cancers in people of all ages, and its grade recognition is a challenging problem for radiologists in health monitoring and automated diagnosis. Recently, numerous methods based on deep learning have been presented in the literature for brain tumor classification (BTC) in order to assist radiologists for a better diagnostic analysis. In this overview, we present an in-depth review of the surveys published so far and recent deep learning-based methods for BTC. Our survey covers the main steps of deep learning-based BTC methods, including preprocessing, features extraction, and classification, along with their achievements and limitations. We also investigate the state-of-the-art convolutional neural network models for BTC by performing extensive experiments using transfer learning with and without data augmentation. Furthermore, this overview describes available benchmark data sets used for the evaluation of BTC. Finally, this survey does not only look into the past literature on the topic but also steps on it to delve into the future of this area and enumerates some research directions that should be followed in the future, especially for personalized and smart healthcare.
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

DNA N4-methylcytosine (4mC) is an important epigenetic modification that plays a vital role in regulating DNA replication and expression. However, it is challenging to detect 4mC sites through experimental methods, which are time-consuming and costly. Thus, computational tools that can identify 4mC sites would be very useful for understanding the mechanism of this important type of DNA modification. Several machine learning-based 4mC predictors have been proposed in the past 3 years, although their performance is unsatisfactory. Deep learning is a promising technique for the development of more accurate 4mC site predictions. In this work, we propose a deep learning-based approach, called DeepTorrent, for improved prediction of 4mC sites from DNA sequences. It combines four different feature encoding schemes to encode raw DNA sequences and employs multi-layer convolutional neural networks with an inception module integrated with bidirectional long short-term memory to effectively learn the higher-order feature representations. Dimension reduction and concatenated feature maps from the filters of different sizes are then applied to the inception module. In addition, an attention mechanism and transfer learning techniques are also employed to train the robust predictor. Extensive benchmarking experiments demonstrate that DeepTorrent significantly improves the performance of 4mC site prediction compared with several state-of-the-art methods.
Effects of Plyometric and Repeated Sprint Training on Physical Performance

The purpose of study was to resolve the effect of plyometric training and repeated sprint training on physical performance. The study was conducted on 41 subjects in two experimental groups (plyometric/repeated sprints training). Before and after the training program, subjects were subjected to diagnostic procedures that included standard test protocols. Results proved a statistically significant difference only after the plyometric training program compared to the repeated sprint group in countermovement jump (8.65% vs. 2.21%). In variable repeated jumps, an increased value was recorded (2.9% vs. 4.29%), like in sprint variables after the training program where certain trends of progress happened after the repeated sprint ability training and the specificity of the program (5 m = 0.89%, 10 m = 1.07% and 25 m = 1.35%), while plyometric training recorded unchanged values at 5 and 10 m, and a 0.27% improvement at 25 m. Stagnation of the 20-yard test was recorded in both groups. There was no difference between training programs in any variables of functional capacities, with similar measures recorded in repeated sprint ability. After six weeks of both training types, positive changes can be expected in explosive strength of lower extremities, increases in acceleration area, and maximum speed.
FOREST ECOSYSTEM CARBON AND NITROGEN ACCUMULATION DURING THE FIRST CENTURY AFTER AGRICULTURAL ABANDONMENT

Forests of the northeastern United States are expected to serve as a substantial sink for carbon (C) and nitrogen (N) as they recover from extensive clearing and agriculture. However, questions remain concerning the rate, distribution, and duration of this potential sink. We used a chronosequence approach to determine changes in ecosystem C and N during the first 115 years of forest development after agricultural abandonment in Rhode Island, USA. All sites had similar soils, climate, land-use history, and dominant overstory vegetation (Pinus strobus), but differed in time since agricultural abandonment. Total ecosystem C increased linearly across the chronosequence at a mean rate of 2.10 Mg C·ha–1·yr–1. Most of the C was sequestered into plant biomass (73%) with less stored in the forest floor (17%) and deep mineral soil (6%; 20–70 cm depth). Total ecosystem N did not change over time; instead N accumulated in the forest floor (11.6 kg N·ha–1·yr–1) and plant biomass (4.1 kg N·ha–1·yr–1), and these increas.
Simple, Accurate and User-Friendly Differential Constitutive Model for the Rheology of Entangled Polymer Melts and Solutions from Nonequilibrium Thermodynamics

In a recent reformulation of the Marrucci-Ianniruberto constitutive equation for the rheology of entangled polymer melts in the context of nonequilibrium thermodynamics, rather large values of the convective constraint release parameter βccr had to be used in order for the model not to violate the second law of thermodynamics. In this work, we present an appropriate modification of the model, which avoids the splitting of the evolution equation for the conformation tensor into an orientation and a stretching part. Then, thermodynamic admissibility simply dictates that βccr ≥ 0, thus allowing for more realistic values of βccr to be chosen. Moreover, and in view of recent experimental evidence for a transient stress undershoot (following the overshoot) at high shear rates, whose origin may be traced back to molecular tumbling, we have incorporated additional terms into the model accounting, at least in an approximate way, for non-affine deformation through a slip parameter ξ. Use of the new model to describe available experimental data for the transient and steady-state shear and elongational rheology of entangled polystyrene melts and concentrated solutions shows close agreement. Overall, the modified model proposed here combines simplicity with accuracy, which renders it an excellent choice for managing complex viscoelastic fluid flows in large-scale numerical calculations.