Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Expansion of Chondrocytes

Summary A n alternative therapy for the repair of damaged articular cartilage resides in the tissue engineering approach. However, routine tissue culture methodologies can hardly cope with the scale of cell production required for the manufacture of engineered cartilage tissue products. Consequently, in vitro cell expansion has become an essential step in the process of tissue engineering of articular cartilage and the optimization of expansion protocols is a fundamental issue that needs to be addressed. In particular, both the finding of alternative sources of stem/progenitor cells and the development of feasible large scale cell expansion processes are mandatory requirements for a sufficient production of chondrocytes. In this review we delineate the progress that has been made to date and the challenges remaining for the successful production of the large number of articular chondrocytes that would be eventually required by the cartilage tissue engineering industry.
n-Nucleotide circular codes in graph theory

The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons {TAA,TAG,TGA}) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C3 self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156–177. (doi:10.1016/j.jtbi.2015.04.009); Arquès & Michel 1996 J. Theor. Biol. 182, 45–58. (doi:10.1006/jtbi.1996.0142)) and the finding of X circular code motifs in tRNAs and rRNAs, in particular in the ribosome decoding centre (Michel 2012 Comput. Biol. Chem. 37, 24–37. (doi:10.1016/j.compbiolchem.2011.10.002); El Soufi & Michel 2014 Comput. Biol. Chem. 52, 9–17. (doi:10.1016/j.compbiolchem.2014.08.001)). The univerally conserved nucleotides A1492 and A1493 and the conserved nucleotide G530 are included in X circular code motifs. Recently, dinucleotide circular codes were also investigated (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631); Fimmel et al. 2015 J. Theor. Biol. 386, 159–165. (doi:10.1016/j.jtbi.2015.08.034)). As the genetic motifs of different lengths are ubiquitous in genes and genomes, we introduce a new approach based on graph theory to study in full generality n-nucleotide circular codes X, i.e. of length 2 (dinucleotide), 3 (trinucleotide), 4 (tetranucleotide), etc. Indeed, we prove that an n-nucleotide code X is circular if and only if the corresponding graph is acyclic. Moreover, the maximal length of a path in corresponds to the window of nucleotides in a sequence for detecting the correct reading frame. Finally, the graph theory of tournaments is applied to the study of dinucleotide circular codes. It has full equivalence between the combinatorics theory (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631)) and the group theory (Fimmel et al. 2015 J. Theor. Biol. 386, 159–165. (doi:10.1016/j.jtbi.2015.08.034)) of dinucleotide circular codes while its mathematical approach is simpler.
Assigning Weights to Minimize the Covering Radius in the Plane

Given a set $P$ of $n$ points in the plane and a multiset $W$ of $k$ weights with $k\leq n$, we assign each weight in $W$ to a distinct point in $P$ to minimize the maximum weighted distance from the weighted center of $P$ to any point in $P$. In this paper, we give two algorithms which take $O(k^2n^2\log^3 n)$ time and $O(k^5n\log^3k+kn\log^3 n)$ time, respectively. For a constant $k$, the second algorithm takes only $O(n\log^3n)$ time, which is near linear.
Ecological niche modeling of the genus Papio.

OBJECTIVE Ecological niche modeling (ENM) has been used to assess how abiotic variables influence species distributions and diversity. Baboons are broadly distributed throughout Africa, yet the degree of climatic specialization is largely unexplored for individual taxa. Also, the influence of climate on baboon phylogenetic divergence is unknown. In this study, we constructed ENMs to investigate how niches vary across Papio species to understand how climatic variables have influenced their biogeography and mode of speciation. MATERIALS AND METHODS We used Maxent to generate ENMs by collating locality data for six Papio species and climate information from WorldClim. In addition, we examined the degree of niche overlap among all possible pairs of taxa, which can provide insight into patterns of species diversity. Lastly, we conducted a Mantel test to assess the relationship between niche overlap and estimated time since divergence. RESULTS Our models performed moderately to extremely well, with a mean area under the curve value of 0.868. The species with the best models include P. papio and P. kindae, whereas P. hamadryas had the poorest models. We found that most species pairs exhibited significantly different niches. Lastly, we found no significant correlation between niche overlap and divergence times. DISCUSSION Niche models had good predictive power, which indicates Papio species distributions are correlated with climatic variables to varying degrees. Significantly little niche overlap and incomplete geographic boundaries suggests these models generally support a parapatric speciation scenario for the genus Papio.
Technical note: Correlation between TQA data trends and TomoHD functional status

TomoTherapy Quality Assurance (TQA) is a software package developed to monitor certain aspects of machine performance. In this study, the TQA quantities or data trends most effective in monitoring energy drifts and magnetron stability were determined respectively. This retrospective study used data collected from three TomoHD units. The TQA modules investigated were Step‐Wedge Helical, Step‐Wedge Static, and Basic Dosimetry. First, the TQA quantities correlated with energy changes (|r|>0.85, where r is the Pearson's correlation coefficient) were found. The corresponding sensitivities to percentage depth dose (PDD) ratio changes were then calculated and compared. Second, the pulse‐by‐pulse dose stability was compared before and after each magnetron replacement using a nonparametric comparison test (Welch's t‐test), and the raw dose profiles were surveyed. In this study, exit detector flatness obtained in Basic Dosimetry was shown to be the most sensitive (r=0.945) to energy changes, followed by the energy differences in Step‐Wedge Static (r=0.942) and Step‐Wedge Helical (r=0.898). The three quantities could detect a PDD ratio change of 5.1×10−4,5.4×10−4, and 7.1×10−4, respectively. Pulse‐by‐Pulse Dose1 from Basic Dosimetry over a one‐week period before and after a magnetron replacement showed a significant difference (p<0.05) in only three of the nine instances. On the other hand, a raw output profile free from discontinuities, frequent dropped pulses and abnormal spikes was found to indicate that the magnetron would continue to function normally for a week 89% of the time. PACS numbers: 87.56. bd, 87.56. Fc, 84.40. Fe
Biological Effects and Clinical Applications of Dwarf Elder (Sambucus ebulus L): A Review

Dwarf elder (Sambucus ebulus L) is one of the best known medicinal herbs since ancient times. In view of its benefits as a widely applicable phytomedicine, it is still used in folk medicine of different parts of the world. In addition to its nutritional values, dwarf elder contains different phytochemicals among which flavonoids and lectins are responsible for most of its therapeutic effects. Dwarf elder has been used for different ailments including: joint pains, cold, wounds, and infections. Nevertheless, recent evidence has revealed its potentials for making attempts at treating cancer and metabolic disorders. This review aimed to provide a comprehensive description of dwarf elder regarding its traditional uses and modern findings which may contribute to the development of novel natural-based therapeutic agents.
Effect of stiffeners on failure analyses of optimally designed perforated steel beams

Perforated steel beams can be optimised by increased beam depth and the moment of inertia combined with a reduced web thickness, favouring the use of original I-section beams. The designers are often confronted with situations where optimisation cannot be carried out effectively, taking account of the buckling risk at web posts, moment-shear transfers and local plastic deformations on the transverse holes of the openings. The purpose of this study is to suggest solutions for reducing these failure risks of tested optimal designed beams under applying loads in a self-reacting frame. The design method for the beams is the hunting search optimisation technique, and the design constraints are implemented from BS 5950 provisions. Therefore, I have aimed to explore the strengthening effects of reinforced openings with ring stiffeners, welded vertical simple plates on the web posts and horizontal plates around the openings on the ultimate load carrying capacities of optimally designed perforated steel beams. Test results have shown that compared to lateral stiffeners, ring and vertical stiffeners significantly increase the load-carrying capacity of perforated steel beams.
Recognition of Phytophthora infestans in potato (Solanum tuberosum L.): Scr74 gene as an example

Abstract Phytophthora infestans is the causal agent of late blight, the most devastating disease of potato worldwide. The P. infestans genome encodes potentially polymorphic genes that evolve continually to evade the recognition of plant R genes, though it has hundreds of predicted and conserved effector proteins recognised by the plant. The gene Scr74 encodes a predicted 74-amino acid secreted cysteine-rich protein belonging to a highly polymorphic gene family within P. infestans. This study screened the recognition of Scr74 genes in wild potato genotypes from August 2013 to January 2014 in the Plant Breeding Laboratory of Wageningen University, the Netherlands. To identify the recognition of the Scr74 gene, we grew potato genotypes in the green house for PVX assays, detached leaf assays and molecular work. Twenty-seven good-quality sequences of the Scr74 gene variant with a length of 74 amino acids were found and more frequent amino acid variation was detected on the mature protein. Seventeen Scr74 constructs were identified as diversified and two effectors were strongly recognised by wild S. verrucosum genotypes via effectoromics from the PVX assay. A strong plant cell death hypersensitive response (HR) was recorded on wild S. verrucosum and S. tuberosum genotypes from the detached leaf assay. This recognition seems to be a useful indicator for the presence of a resistance gene (s) to the polymorphic effectors of P. infestans (as it has seen on Scr74 gene) in the wild potato genotypes.
Alterations in neurovascular coupling following acute traumatic brain injury

Traumatic brain injury (TBI) is a leading cause of mortality and disability worldwide. A challenge for diagnosing and assessing the severity of TBI, however, is that quantitative biomarkers are lacking. We explored potential functional indicators for TBI by noninvasively monitoring sensory-evoked electrical and hemodynamic activity using a novel hybrid optical and electrophysiological measurement approach. By combining diffuse correlation spectroscopy with co-localized electrophysiological measurements in a mouse model of TBI, we observed concomitant alterations in somatosensory-evoked cerebral blood flow and electrical potentials following controlled cortical impact. Injury acutely reduced the amplitude of stimulus-evoked responses, which mostly recovered to baseline values within 30 min; intertrial variability for these parameters was also acutely altered. The kinetics of recovery, however, varied among specific components of the evoked waveforms, and we observed strong correlations between the two measurement modalities for only a select subset of waveform parameters. Overall, our results identify a novel set of potential biomarkers for TBI and demonstrate the utility of combined, noninvasive optical and electrophysiological measurements for detecting injury-induced abnormalities in neurovascular reactivity.
Mining User Reviews for Mobile App Comparisons

As the number of mobile apps keeps increasing, users often need to compare many apps, in order to choose one that best fits their needs. Fortunately, as there are so many users sharing an app market, it is likely that some other users with the same preferences have already made the comparisons and shared their opinions. For example, a user may state that an app is better in power consumption than another app in a review, then the review would help other users who care about battery life while choosing apps. This paper presents a method to identify comparative reviews for mobile apps from an app market, which can be used to provide fine-grained app comparisons based on different topics. According to experiments on 5 million reviews from Google Play and manual assessments on 900 reviews, our method is able to identify opinions accurately and provide meaningful comparisons between apps, which could in turn help users find desired apps based on their preferences.
Selective-Delay Garbage Collection Mechanism for Read Operations in Multichannel Flash-Based Storage Devices

Flash memory has been a dominant storage medium in consumer electronics. Its wide deployment results from the remarkable progress in garbage collection mechanism which resolves the inherent limitation, not-in-place-update property, of flash memory. In this paper, we propose a new garbage collection management scheme, called selective-delay garbage collection, which can be used to optimize read operations. In our proposal, garbage collections are allowed to proceed only if they do not block the execution of incoming read operations. For this, the proposed scheme cooperates with an event queue in storage devices of consumer electronics. When read operations in the event queue are likely to collide with a garbage collection request, the read operations are processed preferentially by delaying garbage collection. This reduces the average read latency by avoiding time-consuming garbage collections. The experimental results with realistic workloads show that average read latency decreases by up to 13.53%, and the time elapsed by garbage collections is reduced by up to 78.37%, whereas the increase in write latency is limited to 0.83%.
Single Stage Management of Concomitant Cholelithiasis and Choledocholithiasis.

INTRODUCTION Concomitant cholelithiasis and choledocholithiasis are commonly managed in two stage procedure, endoscopic management of common bile duct stone followed by laparoscopic cholecystectomy in different time and setting. We perform these two procedures in same sitting in operating room set up. We evaluated the procedure in terms of outcome, feasibility and complications. METHODS Prospective cross-sectional study carried out since April 2013 to August 2016 in all patients who had undergone single stage endoscopic and laparoscopic management of concomitant cholelithiasis and choledocholithiasis. Patient's demography, procedural time for different procedure and procedure in total and post-operative complications were recorded and analyzed with suitable statistical methods. RESULTS Out of 50 cases enrolled, 2 patients were converted to open. Out of 48 patients, 3 needed re-attempt for completion. Majority were female 36 (72%), mean age was 39.48years. Mean common bile duct diameter and mean stone size was 11.43±2.63 cm and 7.99±2.01cm, respectively. Mean of total procedural time was 90.93± 33.68 minutes. In most of the cases, laparoscopic cholecystectomy performed first followed by endoscopic method (66.7%). Total procedural time was less in the patients who underwent laparoscopy first in comparison to endoscopy first. Clinically significant complications like cholangitis, pancreatitis and duodenal perforation occurred in 7 patients. Out of 4 patients who developed pancreatitis, one had severe acute pancreatitis requiring prolonged hospitalization. CONCLUSION Single stage management of common bile duct and gall bladder stone by laparoscopic and endoscopic method is feasible in our setup with acceptable results. Endoscopic treatment of common bile duct stone if performed first, is associated with longer procedural time.
Stable and Compliant Motion of Physical Human–Robot Interaction Coupled With a Moving Environment Using Variable Admittance and Adaptive Control

There are an increasing number of applications that require the end-effector of a robotic manipulator to be compliant in response to the intended force exerted by a human operator. In physical human–robot interaction, the stability and compliance are often affected in the presence of both human and an environment, especially during the transition from noncontact to contact. Unlike previous works, the physical human–robot interaction in this letter takes into consideration of the interaction of the human, robot, and a moving environment. To achieve this, this letter proposes a variable admittance control strategy with an adaptive controller to produce a time-varying stiffness interacting with the human and a moving environment simultaneously. The passivity of the system is guaranteed for time-varying admittance with human interaction coupled with a moving environment. Experiments are conducted to demonstrate the capability of the controller.
Parental Adverse Childhood Experiences and Offspring Development at 2 Years of Age

In a suburban pediatric primary care population, maternal and paternal ACEs were associated with an increased risk for offspring developmental delay at 24 months. OBJECTIVES: The study objective was to determine if maternal and paternal exposure to adverse childhood experiences (ACEs) have a significant association with negative offspring development at 24 months of age in a suburban pediatric primary care population. METHODS: A retrospective cohort study was conducted of 311 mother-child and 122 father-child dyads who attended a large pediatric primary care practice. Children were born from October 2012 to June 2014, and data were collected at the 2-, 4-, and 24-month well-child visits. Multivariable Poisson regression with robust error variance was used to model the relationship between self-reported parental ACEs and the outcomes of suspected developmental delay at 24 months and eligibility for early intervention services. RESULTS: For each additional maternal ACE, there was an 18% increase in the risk for a suspected developmental delay (relative risk: 1.18, 95% confidence interval: 1.08–1.29). A similar trend was observed for paternal ACEs (relative risk: 1.34, 95% confidence interval: 1.07–1.67). Three or more maternal ACEs (versus <3 ACEs) was associated with a significantly increased risk for a suspected developmental delay that affected multiple domains. Similar effects were observed for early intervention services. CONCLUSIONS: Parental ACE exposures can negatively impact child development in multiple domains, including problem solving, communication, personal-social, and motor skills. Research is needed to elucidate the psychosocial and biological mechanisms of intergenerational risk. This research has implications for the value of parental ACE screening in the context of pediatric primary care.
Distinct mechanistic responses to replication fork stalling induced by either nucleotide or protein deprivation

ABSTRACT Incidents that slow or stall replication fork progression, collectively known as replication stress, represent a major source of spontaneous genomic instability. Here, we determine the requirement for global protein biosynthesis on DNA replication and associated downstream signaling. We study this response side by side with dNTP deprivation; one of the most commonly used means to investigate replication arrest and replicative stress. Our in vitro interrogations reveal that inhibition of translation by cycloheximide (CHX) rapidly impairs replication fork progression without decoupling helicase and polymerase activities or inducing DNA damage. In line with this, protein deprivation stress does not activate checkpoint signaling. In contrast to the direct link between insufficient dNTP pools and genome instability, our findings suggest that replication forks remain stable during short-term protein deficiency. We find that replication forks initially endure fluctuations in protein supply in order to efficiently resume DNA synthesis upon reversal of the induced protein deprivation stress. These results reveal distinct cellular responses to replication arrest induced by deprivation of either nucleotides or proteins.
Learning With Augmented Features for Supervised and Semi-Supervised Heterogeneous Domain Adaptation

In this paper, we study the heterogeneous domain adaptation (HDA) problem, in which the data from the source domain and the target domain are represented by heterogeneous features with different dimensions. By introducing two different projection matrices, we first transform the data from two domains into a common subspace such that the similarity between samples across different domains can be measured. We then propose a new feature mapping function for each domain, which augments the transformed samples with their original features and zeros. Existing supervised learning methods (e.g., SVM and SVR) can be readily employed by incorporating our newly proposed augmented feature representations for supervised HDA. As a showcase, we propose a novel method called Heterogeneous Feature Augmentation (HFA) based on SVM. We show that the proposed formulation can be equivalently derived as a standard Multiple Kernel Learning (MKL) problem, which is convex and thus the global solution can be guaranteed. To additionally utilize the unlabeled data in the target domain, we further propose the semi-supervised HFA (SHFA) which can simultaneously learn the target classifier as well as infer the labels of unlabeled target samples. Comprehensive experiments on three different applications clearly demonstrate that our SHFA and HFA outperform the existing HDA methods.
Combining Optogenetics with Artificial microRNAs to Characterize the Effects of Gene Knockdown on Presynaptic Function within Intact Neuronal Circuits

The purpose of this protocol is to characterize the effect of gene knockdown on presynaptic function within intact neuronal circuits. We describe a workflow on how to combine artificial microRNA (miR)-mediated RNA interference with optogenetics to achieve selective stimulation of manipulated presynaptic boutons in acute brain slices. The experimental approach involves the use of a single viral construct and a single neuron-specific promoter to drive the expression of both an optogenetic probe and artificial miR(s) against presynaptic gene(s). When stereotactically injected in the brain region of interest, the expressed construct makes it possible to stimulate with light exclusively the neurons with reduced expression of the gene(s) under investigation. This strategy does not require the development and maintenance of genetically modified mouse lines and can in principle be applied to other organisms and to any neuronal gene of choice. We have recently applied it to investigate how the knockdown of alternative splice isoforms of presynaptic P/Q-type voltage-gated calcium channels (VGCCs) regulates short-term synaptic plasticity at CA3 to CA1 excitatory synapses in acute hippocampal slices. A similar approach could also be used to manipulate and probe the neuronal circuitry in vivo.