Miracle-dz/UniFAR-FTUs huggingface dataset:
Backscattered electron SEM imaging of resin sections from plant specimens: observation of histological to subcellular structure and CLEM

We have refined methods for biological specimen preparation and low‐voltage backscattered electron imaging in the scanning electron microscope that allow for observation at continuous magnifications of ca. 130–70 000 X, and documentation of tissue and subcellular ultrastructure detail. The technique, based upon early work by Ogura & Hasegawa (1980), affords use of significantly larger sections from fixed and resin‐embedded specimens than is possible with transmission electron microscopy while providing similar data. After microtomy, the sections, typically ca. 750 nm thick, were dried onto the surface of glass or silicon wafer and stained with heavy metals—the use of grids avoided. The glass/wafer support was then mounted onto standard scanning electron microscopy sample stubs, carbon‐coated and imaged directly at an accelerating voltage of 5 kV, using either a yttrium aluminum garnet or ExB backscattered electron detector. Alternatively, the sections could be viewed first by light microscopy, for example to document signal from a fluorescent protein, and then by scanning electron microscopy to provide correlative light/electron microscope (CLEM) data. These methods provide unobstructed access to ultrastructure in the spatial context of a section ca. 7 × 10 mm in size, significantly larger than the typical 0.2 × 0.3 mm section used for conventional transmission electron microscopy imaging. Application of this approach was especially useful when the biology of interest was rare or difficult to find, e.g. a particular cell type, developmental stage, large organ, the interface between cells of interacting organisms, when contextual information within a large tissue was obligatory, or combinations of these factors. In addition, the methods were easily adapted for immunolocalizations.
How Does Tree Density Affect Water Loss of Peatlands? A Mesocosm Experiment

Raised bogs have accumulated more atmospheric carbon than any other terrestrial ecosystem on Earth. Climate-induced expansion of trees and shrubs may turn these ecosystems from net carbon sinks into sources when associated with reduced water tables. Increasing water loss through tree evapotranspiration could potentially deepen water tables, thus stimulating peat decomposition and carbon release. Bridging the gap between modelling and field studies, we conducted a three-year mesocosm experiment subjecting natural bog vegetation to three birch tree densities, and studied the changes in subsurface temperature, water balance components, leaf area index and vegetation composition. We found the deepest water table in mesocosms with low tree density. Mesocosms with high tree density remained wettest (i.e. highest water tables) whereas the control treatment without trees had intermediate water tables. These differences are attributed mostly to differences in evapotranspiration. Although our mesocosm results cannot be directly scaled up to ecosystem level, the systematic effect of tree density suggests that as bogs become colonized by trees, the effect of trees on ecosystem water loss changes with time, with tree transpiration effects of drying becoming increasingly offset by shading effects during the later phases of tree encroachment. These density-dependent effects of trees on water loss have important implications for the structure and functioning of peatbogs.
Urinary [TIMP‐2] × [IGFBP7] for risk prediction of acute kidney injury in decompensated heart failure

In acute decompensated heart failure (ADHF) the risk of acute kidney injury (AKI) is high. Early detection of patients at risk for AKI is important. We tested urinary [TIMP‐2] × [IGFBP7], a new US Food and Drug Administration–cleared test to assess AKI risk, in a cohort of hospitalized ADHF patients.
Potential Bud Bank Responses to Apical Meristem Damage and Environmental Variables: Matching or Complementing Axillary Meristems?

Soil nutrients, dormant axillary meristem availability, and competition can influence plant tolerance to damage. However, the role of potential bud banks (adventitious meristems initiated only after injury) is not known. Examining Central European field populations of 22 species of short-lived monocarpic herbs exposed to various sources of damage, we hypothesized that: (1) with increasing injury severity, the number of axillary branches would decrease, due to axillary meristem limitation, whereas the number of adventitious shoots (typically induced by severe injury) would increase; (2) favorable environmental conditions would allow intact plants to branch more, resulting in stronger axillary meristem limitation than in unfavorable conditions; and (3) consequently, adventitious sprouting would be better enabled in favorable than unfavorable conditions. We found strong support for the first hypothesis, only limited support for the second, and none for the third. Our results imply that whereas soil nutrients and competition marginally influence plant tolerance to damage, potential bud banks enable plants to overcome meristem limitation from severe damage, and therefore better tolerate it. All the significant effects were found in intraspecific comparisons, whereas interspecific differences were not found. Monocarpic plants with potential bud banks therefore represent a distinct strategy occupying a narrow environmental niche. The disturbance regime typical for this niche remains to be examined, as do the costs associated with the banks of adventitious and axillary reserve meristems.
Comparison of planned menus and centre characteristics with foods and beverages served in New York City child-care centres

Abstract Objective The present study evaluated the extent to which child-care centre menus prepared in advance correspond with food and beverage items served to children. The authors identified centre and staff characteristics that were associated with matches between menus and what was served. Design Menus were collected from ninety-five centres in New York City (NYC). Direct observation of foods and beverages served to children were conducted during 524 meal and snack times at these centres between April and June 2010, as part of a larger study designed to determine compliance of child-care centres with city health department regulations for nutrition. Setting Child-care centres were located in low-income neighbourhoods in NYC. Results Overall, 87 % of the foods and beverages listed on the menus or allowed as substitutions were served. Menu items matched with foods and beverages served for all major food groups by >60 %. Sweets and water had lower match percentages (40 and 32 %, respectively), but water was served 68 % of the time when it was not listed on the menu. The staff person making the food and purchasing decisions predicted the match between the planned or substituted items on the menus and the foods and beverages served. Conclusions In the present study, child-care centre menus included most foods and beverages served to children. Menus planned in advance have potential to be used to inform parents about which child-care centre to send their child or what foods and beverages their enrolled children will be offered throughout the day.
Minimally Invasive Distal Metatarsal Metaphyseal Osteotomy (DMMO) of the Fifth Metatarsal for Bunionette Correction

Background: Different osteotomies have been proposed for the treatment of bunionette deformity. Minimally invasive surgery is now increasingly popular for a variety of forefoot conditions. The aim of this study was to evaluate the outcome following fifth minimally invasive distal metatarsal metaphyseal osteotomy (DMMO) for bunionette deformity. Methods: Nineteen patients (21 feet) who had symptomatic bunionette deformity and failed conservative treatment between 2014 and 2016 were included in this retrospective study. Clinical data were recorded, and pre- and postoperative Manchester-Oxford Foot Questionnaire (MOXFQ) scores and visual analog scale (VAS) pain score were collected. The mean follow-up was 28 months (range, 12-47). Results: The mean MOXFQ summary index score decreased from 71 (range, 59-81) preoperatively to 10 (range, 0-30) postoperatively. All 3 MOXFQ domains also improved. The average improvement in VAS score was 7. Forefoot swelling and some painful symptoms took an average of 3 months to settle. There were no wound or nerve complications. One patient required a dorsal cheilectomy for a symptomatic prominent dorsolateral callus formation. Conclusion: The minimally invasive fifth DMMO for bunionette deformity was a safe and effective technique. It had relatively few complications and led to good clinical results. We believe it is important to warn patients that the forefoot swelling will take months to settle compared to an osteotomy with fixation, and there is a 10% chance of a prominent callus over the osteotomy site. Level of Evidence: Level IV, retrospective case series.
Cardiovascular magnetic resonance imaging and clinical performance of somatostatin receptor positron emission tomography in cardiac sarcoidosis

Cardiac affection constitutes a major limiting condition in systemic sarcoidosis. The primary objective of this study was to investigate the persistence rate of cardiac sarcoid involvement by cardiovascular magnetic resonance (CMR) imaging in patients diagnosed with cardiac sarcoidosis (CS). Moreover, we examined the additional insights into myocardial damage's characteristics gained by somatostatin receptor scintigraphy.
Variety in Parental Use of “Want” Relates to Subsequent Growth in Children’s Theory of Mind

In 2 cross-lagged, longitudinal studies we contrasted parental talk about want in a single context versus multiple contexts. Study 1 examined thirty-two 2 year olds, with mothers describing pictures to children. Mothers could use want in zero, one, or multiple contexts. Children whose mothers used want in multiple contexts experienced a significantly larger gain in mental state terms over a 6-month period. Study 2 examined 50 preschoolers, measuring theory of mind (ToM) with tasks and mental state terms, then had parents intervene by reading booklets in which want was used in 1 or multiple contexts. Over a 6-week period, the latter group made larger gains in ToM. We posit that maternal use of want in multiple contexts assists understanding that want refers to an underlying mental state rather than a single behavior.
[Glioblastoma metastases: a literature review and a description of six clinical observations].

INTRODUCTION since the 1990s, the literature has described cases of glioblastoma metastases with the development of foci located at a distance from the primary tumor. However, the pathogenesis of this process remains unclear until the end. This focus is believed to result, on the one hand, from tumor metastasis from the primary site and, on the other hand, from multifocal growth. This article presents a literature review and a description of clinical observations of patients with glioblastoma metastases. MATERIAL AND METHODS The study included 6 patients (1 female and 5 males) with brain glioblastomas who received treatment at the Burdenko Neurosurgical Institute (5 patients) and the Department of Neurosurgery of the Research Center of Neurology (1 patient) in the period from 2010 to 2014. Neurophysiological control was used if the tumor was localized near the eloquent cortical areas and pathways; 4 of 6 patients were operated on using the methods of intraoperative fluorescence diagnosis (5-ALA agent--Alasens). RESULTS Four patients had metastases within one hemisphere, two had metastases in the contralateral hemisphere in the period of 5 to 18 months after the first operation. The primary tumor site was located near the ventricular system in two patients. In one patient, the lateral ventricle was opened during the first operation. In another patient, the prepontine cistern was opened during the first operation. In two patients, the primary tumor site was located at a distance from the lateral ventricles, however, the tumor was located near them during recurrence. Based on metabolic navigation, fluorescence of the tumor was observed in the four patients during both the first and repeated operations. CONCLUSIONS The close relationship between primary glioblastomas and metastases and the cerebrospinal fluid circulation pathways may confirm the fact of dissemination of tumor cells with cerebrospinal fluid flow. In our opinion, there should be an increased suspicion of the possibility for metastases of glioblastomas that are closely associated with the cerebrospinal fluid circulation pathways. Metabolic navigation with 5-ALA is effective both during primary surgery in patients with glioblastomas and during resection of glioblastoma metastases.
Targeting AXL and mTOR Pathway Overcomes Primary and Acquired Resistance to WEE1 Inhibition in Small-Cell Lung Cancer

Purpose: Drugs targeting DNA repair and cell-cycle checkpoints have emerged as promising therapies for small-cell lung cancer (SCLC). Among these, the WEE1 inhibitor AZD1775 has shown clinical activity in a subset of SCLC patients, but resistance is common. Understanding primary and acquired resistance mechanisms will be critical for developing effective WEE1 inhibitor combinations. Experimental Design: AZD1775 sensitivity in SCLC cell lines was correlated with baseline expression level of 200 total or phosphorylated proteins measured by reverse-phase protein array (RPPA) to identify predictive markers of primary resistance. We further established AZD1775 acquired resistance models to identify mechanism of acquired resistance. Combination regimens were tested to overcome primary and acquired resistance to AZD1775 in in vitro and in vivo SCLC models. Results: High-throughput proteomic profiling demonstrate that SCLC models with primary resistance to AZD1775 express high levels of AXL and phosphorylated S6 and that WEE1/AXL or WEE1/mTOR inhibitor combinations overcome resistance in vitro and in vivo. Furthermore, AXL, independently and via mTOR, activates the ERK pathway, leading to recruitment and activation of another G2-checkpoint protein, CHK1. AZD1775 acquired resistance models demonstrated upregulation of AXL, pS6, and MET, and resistance was overcome with the addition of AXL (TP0903), dual-AXL/MET (cabozantinib), or mTOR (RAD001) inhibitors. Conclusions: AXL promotes resistance to WEE1 inhibition via downstream mTOR signaling and resulting activation of a parallel DNA damage repair pathway, CHK1. These findings suggest rational combinations to enhance the clinical efficacy of AZD1775, which is currently in clinical trials for SCLC and other malignancies. Clin Cancer Res; 23(20); 6239–53. ©2017 AACR.
Alignment of dynamic networks

Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well‐ to poorly‐studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real‐world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof‐of‐concept dynamic NA method is an extension of a state‐of‐the‐art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state‐of‐the‐art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real‐world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user‐friendly graphical interface. Availability and implementation: http://nd.edu/˜cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
The Impact of Postoperative Enteral Immunonutrition on Postoperative Complications and Survival in Gastric Cancer Patients – Randomized Clinical Trial

ABSTRACT Background: Immunomodulating enteral nutrition in the perioperative period may reduce postoperative complications in cancer patients. Little is known if this effect translates to the better survival. The aim of study was to assess the impact of postoperative immunomodulating enteral nutrition on postoperative complications and survival of gastric cancer patients. Methods: A group of 98 gastric cancer patients was randomly assigned for postoperative immunomodulating enteral nutrition n = 44 (Reconvan, Fresenius Kabi, Bad Homburg, Germany), or standard enteral nutrition n = 54 (Peptisorb, Nutricia, Schipol, The Netherlands). Postoperative complications, mortality, 6-mo and 1-yr survival were analyzed. Results: The overall postoperative morbidity did not differ between the groups. The rate of pulmonary complications (excluding pneumonia) was significantly lower in immunomodulation group (0% vs 9.3%, p = 0.044), as well as 60-day mortality (0% vs. 11.1%, p = 0.037). There was no difference in 6-mo and 1-yr survival between the groups. Conclusions: Postoperative immunomodulating enteral nutrition may reduce respiratory complications and postoperative mortality in comparison to standard enteral nutrition. Despite this effect, it did not improve 6-mo and 1-yr survival in immunomodulation group. Probably the beneficial effect of immunomodulating enteral nutrition is too weak to be significant in such a number of patients.
Robust Reputation-Based Ranking on Bipartite Rating Networks

With the growth of the Internet and E-commerce, bipartite rating networks are ubiquitous. In such bipartite rating networks, there exist two types of entities: the users and the objects, where users give ratings to objects. A fundamental problem in such networks is how to rank the objects by user’s ratings. Although it has been extensively studied in the past decade, the existing algorithms either cannot guarantee convergence, or are not robust to the spammers. In this paper, we propose six new reputation-based algorithms, where the users’ reputation is determined by the aggregated difference between the users’ ratings and the corresponding objects’ rankings. We prove that all of our algorithms converge into a unique fixed point. The time and space complexity of our algorithms are linear w.r. t. the size of the graph, thus they can be scalable to large datasets. Moreover, our algorithms are robust to the spamming users. We evaluate our algorithms using three real datasets. The experimental results confirm the effectiveness, efficiency, and robustness of our algorithms.
Virus versus Host Plant MicroRNAs: Who Determines the Outcome of the Interaction?

Considering the importance of microRNAs (miRNAs) in the regulation of essential processes in plant pathogen interactions, it is not surprising that, while plant miRNA sequences counteract viral attack via antiviral RNA silencing, viruses in turn have developed antihost defense mechanisms blocking these RNA silencing pathways and establish a counter-defense. In the current study, computational and stem-loop Reverse Transcription – Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5′/3′ harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. Different viral pre-miRNA hairpin sequences and viral miR/miR* length variants occurring as isomiRs were predicted in both viruses. These miRNAs were located in three Open Reading Frames (ORFs) and in the Intergenic Region (IR). Moreover, various target genes for miRNAs from both viruses were predicted and annotated in the host plant genomes indicating that they are involved in biotic response, metabolic pathways and transcription factors. Plant miRs/miRs* from conserved and highly expressed families were identified, which were shown to have potential targets in the genome of both begomoviruses, representing potential plant miRNAs mediating antiviral defense. This is the first assessment of predicted viral miRs/miRs* of ACMV and EACMV-UG and host plant miRNAs, providing a reference point for miRNA identification in pathogens and their hosts. These findings will improve the understanding of host- pathogen interaction pathways and the function of viral miRNAs in Euphorbiaceous crop plants.
Post-Surgical Analgesia in Rainbow Trout: Is Reduced Cardioventilatory Activity a Sign of Improved Animal Welfare or the Adverse Effects of an Opioid Drug?

The use of fish models in biomedical research is increasing. Since behavioural and physiological consequences of surgical procedures may affect experimental results, these effects should be defined and, if possible, ameliorated. Thus, the use of post-surgical analgesia should be considered after invasive procedures also in fish, but presently, little information exists on the effects of analgesics in fish. This study assessed the effects of an opioid drug, buprenorphine (0.05 mg/kg IM), on resting ventilation and heart rates during 7 days of postsurgical recovery in rainbow trout (Oncorhynchus mykiss) at 10°C by non-invasively recording bioelectric potentials from the fish via electrodes in the water. Baseline ventilation and heart rates were considerably lower compared to previously reported values for rainbow trout at 10°C, possibly due to the non-invasive recording technique. Buprenorphine significantly decreased both ventilation and heart rates further, and the effects were most pronounced at 4–7 days after anaesthesia, surgical procedures and administration of the drug. Somewhat surprisingly, the same effects of buprenorphine were seen in the two control groups that had not been subject to surgery. These results indicate that the reductions in ventilation and heart rates are not caused by an analgesic effect of the drug, but may instead reflect a general sedative effect acting on both behaviour as well as e.g. central control of ventilation in fishes. This resembles what has previously been demonstrated in mammals, although the duration of the drug effect is considerably longer in this ectothermic animal. Thus, before using buprenorphine for postoperative analgesic treatment in fish, these potentially adverse effects need further characterisation.