Miracle-dz/UniFAR-FTUs huggingface dataset:
Chondrogenic Differentiation Capacity of Human Umbilical Cord Mesenchymal Stem Cells with Platelet Rich Fibrin Scaffold in Cartilage Regeneration (In Vitro Study)

Background: Human umbilical cord mesenchymal stem cell is a promising source of allogenous MSC with great chondrogenic differentiation capacity. Meanwhile, platelet rich fibrin (PRF) is a natural fibrin matrix, rich in growth factors, forming a smooth and flexible fibrin network, supporting cytokines and cell migration, thus can be used as a scaffold that facilitate the differentiation of MSC. However, the differential capability of MSC cultured in PRF was still poorly understood. Method: We studied in vitro differentiation potential of MSC cultured in PRF by evaluating several markers such as FGF 18, Sox 9, type II collagen, aggrecan in 3 different culture medium. Result: The result showed that there was positive expression of FGF 18, Sox 9, type II collagen, aggrecan in all medium of in vitro culture. Conclusion: MSC cultured from human umbilical cord had the capacity of chondrogenic differentiation and able to produce cartilage extracellular matrix in vitro which means that hUCMSC is a potential allogeneic MSC for cartilage regeneration.
From ‘cuy' in South America to ‘cavy' in sub-Sahara Africa: Advancing development through South-South Cooperation

1 University of Göttingen, Grisebachstr.6, D-37083 Göttingen, Germany; Email: Brigitte.Maass@yahoo.com 2 INIA (Instituto Nacional de Innovación Agraria), Apartado Postal 2791, Lima 1, Peru; Email: lchauca@inia.gob. pe 3 University of Laikipia, PO Box 1100-20300, Nyahururu, Kenya; Email: chiuriw@gmail.com 4 BecA ILRI (Biosciences eastern and central Africa – International Livestock Research Institute) Hub, PO Box 30709, Nairobi 00100, Kenya; Email: A.Djikeng@cgiar.org 5 University of Dschang, PO Box 188, Dschang, Cameroon; Email: fmeutchieye@univ-dschang.org 6 Pengelly Consultancy, Brisbane, Australia; Email: bruce.pengelly@gmail.com 7 Bioversity International, Via dei Tre Denari 472/a, 00057 Maccarese, Rome, Italy; Email: C.Sere@cgiar.org * Corresponding author
Dual blockade of aldosterone and angiotensin II additively suppresses TGF-beta and NADPH oxidase in the hypertensive kidney.

BACKGROUND Angiotensin II blockade and spironolactone effectively reduces proteinuria in humans. To clarify the mechanisms of the beneficial effect of blockade of both aldosterone and angiotensin II, we associated the aldosterone antagonist eplerenone to an angiotensin-converting enzyme inhibitor (ACEI) and examined the effect on renal transforming growth factor (TGF)-beta expression and oxidative stress by nicotinamide adenine dinucleotide phosphate (NADPH) oxidase in the Dahl salt-sensitive rat with heart failure (DSHF). METHODS Dahl salt-resistant control rats and DSHF rats were fed with 8% NaCl diet and at 11 weeks the DSHF rats were treated with vehicle, eplerenone (Epl), trandolapril or a combination of both drugs for 7 weeks. RESULTS DSHF rats showed increased NADPH oxidase and decreased superoxide dismutase (SOD) resulting in increased oxidative stress. ACEI and Epl reduced NADPH oxidase showing an additive effect in their combination; ACEI increased manganese SOD (MnSOD) and Epl increased MnSOD, copper-zinc SOD and catalase, resulting in the lowest levels of oxidative stress with the combination therapy. Glomerulosclerosis and proteinuria were increased in the DSHF rats, and Epl suppressed them more effectively than ACEI to levels not different from the combination of both, showing a positive correlation with NADPH oxidase expression and TGF-beta. Renal TGF-beta was specifically suppressed with Epl CONCLUSION The association of Epl to ACEI is beneficial due to further reduction of NADPH oxidase and specific inhibition of TGF-beta resulting in improvement of renal damage.
Cell Specific CD44 Expression in Breast Cancer Requires the Interaction of AP-1 and NFκB with a Novel cis-Element

Breast cancers contain a heterogeneous population of cells with a small percentage that possess properties similar to those found in stem cells. One of the widely accepted markers of breast cancer stem cells (BCSCs) is the cell surface marker CD44. As a glycoprotein, CD44 is involved in many cellular processes including cell adhesion, migration and proliferation, making it pro-oncogenic by nature. CD44 expression is highly up-regulated in BCSCs, and has been implicated in tumorigenesis and metastasis. However, the genetic mechanism that leads to a high level of CD44 expression in breast cancer cells and BCSCs is not well understood. Here, we identify a novel cis-element of the CD44 directs gene expression in breast cancer cells in a cell type specific manner. We have further identified key trans-acting factor binding sites and nuclear factors AP-1 and NFκB that are involved in the regulation of cell-specific CD44 expression. These findings provide new insight into the complex regulatory mechanism of CD44 expression, which may help identify more effective therapeutic targets against the breast cancer stem cells and metastatic tumors.
Improvement of the GenTHREADER Method for Genomic Fold Recognition

MOTIVATION In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. RESULTS The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method. AVAILABILITY http://www.psipred. net.
An efficient algorithm for optimum joint downlink beamforming and power control

We address the problem of joint downlink beamforming and power control in a frequency flat multi-antenna broadcast channel. In this context, a common optimization strategy is to maximize the system throughput under a certain power constraint. This, however, does not guarantee a fair sharing of throughput among the users, which is required in case that the receivers cannot cooperate. Thus, we propose a different approach, which always assumes optimally balanced data rates. If the problem is feasible, i.e., desired target rates can be reached, spare degrees of freedom can be used in order to minimize the total transmission power. This strategy can even be applied if only spatial covariance channel information is available. The authors have developed a theoretical framework based upon uplink/downlink duality, feasibility considerations, and bounds on the maximal eigenvalue of the resulting coupling matrix. An overview of the results is given and they are discussed in the context of existing literature. Finally, a theoretical benchmark is provided for the case of perfect channel knowledge. Then, beamforming can be combined with Costa (1983) pre-coding, as proposed by Caire and Shamai (see 36th Asilomar Conf. on Signals, Systems and Computers Asilomar Pacific Grove, CA, Nov. 2001). This leads to a closed-form solution of the problem.
The Neural Basis of Decision-Making and Reward Processing in Adults with Euthymic Bipolar Disorder or Attention-Deficit/Hyperactivity Disorder (ADHD)

Background Attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BD) share DSM-IV criteria in adults and cause problems in decision-making. Nevertheless, no previous report has assessed a decision-making task that includes the examination of the neural correlates of reward and gambling in adults with ADHD and those with BD. Methodology/Principal Findings We used the Iowa gambling task (IGT), a task of rational decision-making under risk (RDMUR) and a rapid-decision gambling task (RDGT) which elicits behavioral measures as well as event-related potentials (ERPs: fERN and P3) in connection to the motivational impact of events. We did not observe between-group differences for decision-making under risk or ambiguity (RDMUR and IGT); however, there were significant differences for the ERP-assessed RDGT. Compared to controls, the ADHD group showed a pattern of impaired learning by feedback (fERN) and insensitivity to reward magnitude (P3). This ERP pattern (fERN and P3) was associated with impulsivity, hyperactivity, executive function and working memory. Compared to controls, the BD group showed fERN- and P3-enhanced responses to reward magnitude regardless of valence. This ERP pattern (fERN and P3) was associated with mood and inhibitory control. Consistent with the ERP findings, an analysis of source location revealed reduced responses of the cingulate cortex to the valence and magnitude of rewards in patients with ADHD and BD. Conclusions/Significance Our data suggest that neurophysiological (ERPs) paradigms such as the RDGT are well suited to assess subclinical decision-making processes in patients with ADHD and BD as well as for linking the cingulate cortex with action monitoring systems.
Cortactin Promotes Migration and PDGF-induced Actin Reorganization by Signaling to Rho-GTPases

Cytoskeleton Dynamics Group, Signalling and Motility Group, Helmholtz Centre for Infection Research, Inhoffen Straße 7, D-38124 Braunschweig, Germany; IFOM Foundation, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Institute of Molecular Biotechnology, Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria; Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany; present address: Department of Developmental and Regenerative Biology, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648; present address: Department of Biology, University ROMA TRE, Viale G. Marconi 446, I-00146, Rome, Italy.
How Genetic Algorithms Really Work I.mutation and Hillclimbing

In this paper mutation and hillclimbing are analyzed with the help of representative binary functions and a simple asexual evolutionary algorithm. An optimal mutation rate is computed and a good agreement t o n umerical results is shown. In most of the cases the optimal mutation rate is proportional to the length of the chromosome. For deceptive functions an evolutionary algorithm with a good hillclimbing strategy and a reasonable mutation rate performs best. The paper is a rst step towards a statistical analysis of genetic algorithms. It shows that the power of mutation has been underestimated in traditional genetic algorithms.
Characteristics of Aggregate Size Distribution of Nanoscale Zero-Valent Iron in Aqueous Suspensions and Its Effect on Transport Process in Porous Media

Bare nanoscale zero-valent iron (NZVI) particles in aqueous suspensions aggregate into micron to submicron sizes. The transport process of enlarged aggregates or multi-sized aggregates is different from that of nanoparticles. In this work, we performed aggregate size distribution analysis of NZVI suspension using a laser grain size analyzer and conducted a series of continuous injection column experiments with different injected NZVI concentrations. The results show that aggregates in NZVI suspensions range from submicron to submillimeter size and are mainly distributed around 5–9 μm and 50–100 μm. Quantitative calculation of iron transport and retention showed that the retained iron linearly correlates with injected concentration. The cross-section images revealed that clogging weakened from inlet to outlet. Furthermore, larger aggregates (>40 μm) appeared more often in the rising-declining stages of breakthrough curves, whereas small aggregates (<30 μm) dominated the steady stage. Indeed, relatively preferential flow facilitated the transport and discharge of both large and small iron aggregates. Straining of glass beads especially for the large iron aggregates resulted in a decline in breakthrough. Moreover, the blocking of attached and plugged iron prevented later retention of iron, resulting in a certain concentration of iron in the effluents. Our study provides greater insight into the transport of NZVI.
Advances in the treatment of Helicobacter pylori infection in children

In this review we elaborate on two main questions concerning the management of Helicobacter pylori infection in children. First, we focus on who should be treated. In the presence of Helicobacter pylori (H. pylori)-associated peptic ulcer disease, eradication of the micro-organism is recommended. When H. pylori infection is detected by biopsy-based methods in the absence of peptic ulcer disease in a child with dyspeptic symptoms, treatment of H. pylori infection may be considered. In infected children whose first degree relatives have gastric cancer, treatment can be offered. A ‘test-and-treat’ strategy is not and has never been recommended in children. The second issue to address is what the recommended treatments are. ESPGHAN/NASPGHAN recommends that treatment tailored to susceptibility testing should be the first choice in pediatric patients. The duration of therapy should be 10-14 days. Costs, compliance and adverse effects should be taken into account. Checking the result of eradication with a reliable non-invasive test such as the 13C urea breath test, is recommended at least 4-8 weeks following completion of therapy.
Motor unit estimations in small muscles of the hand

A quantal method has been employed to determine the numbers of functioning motor units in small muscles of the hand. In healthy subjects below the age of 60 years the mean number of hypothenar motor units was 380 ± 79 and the mean number of thenar units innervated by the median nerve was 340 ± 87. In older subjects there was a progressive reduction in the numbers of functioning units in both muscle groups; in some of these subjects the population of motor units in the extensor digitorum brevis was also estimated for comparison. A study was also performed on patients diagnosed as having generalized denervating diseases or with lesions of peripheral nerves and cervical roots; in every instance the number of functioning motor units was markedly reduced.
Ieee Transactions on Pattern Analysis and Machine Intelligence Describable Visual Attributes for Face Verification and Image Search

—We introduce the use of describable visual attributes for face verification and image search. Describable visual attributes are labels that can be given to an image to describe its appearance. This paper focuses on images of faces and the attributes used to describe them, although the concepts also apply to other domains. Examples of face attributes include gender, age, jaw shape, nose size, etc. The advantages of an attribute-based representation for vision tasks are manifold: they can be composed to create descriptions at various levels of specificity; they are generalizable, as they can be learned once and then applied to recognize new objects or categories without any further training; and they are efficient, possibly requiring exponentially fewer attributes (and training data) than explicitly naming each category. We show how one can create and label large datasets of real-world images to train classifiers which measure the presence, absence, or degree to which an attribute is expressed in images. These classifiers can then automatically label new images. We demonstrate the current effectiveness – and explore the future potential – of using attributes for face verification and image search via human and computational experiments. Finally, we introduce two new face datasets, named FaceTracer and PubFig, with labeled attributes and identities, respectively.
Effects of Anesthesia on Effective Connectivity in the Brain

The brain constitutes a formidably complicated structural network. There are three main types of connectivity used to describe neuronal networks, which reflect three parallel levels of investigation: anatomical connectivity, functional connectivity and effective connectivity. Effective connectivity indicates the direct influence that a node exerts on another, and in the context of neuronal circuits, a causal relationship between the activities of two nodes. Since its definition, effective connectivity analysis has been used to describe causal relationship across multiple spatial scales in PET imaging, fMRI, electroencephalography (EEG) and magnetoencephalography (MEG), single-unit, and local field potential. There are diverse literatures which probe the anesthetized state using effective connectivity analysis over the past two decades. The examination of effective connectivity in the anesthetized state is of relevance to both anesthesiologists and neuroscientists, as it has the potential to elucidate still unclear mechanisms of anesthesia while offering insight into intrinsic functional activity in the brain. The present review attempts to examine, elucidate, and integrate the insight that effective connectivity analysis of the anesthetized state has generated thus far.
Bridge Functionality Relationships for Improved Seismic Risk Assessment of Transportation Networks

Relationships between bridge damage and the resulting loss of functionality of the bridge are critical to assessing the impact of an earthquake event on the performance of the transportation network. This study addresses this data need by use of a Web-based survey of central and southeastern U.S. Department of Transportation bridge inspectors and officials. Results of the 28 responses are analyzed and offer a link between various types of bridge component damage and the expected level of allowable traffic carrying capacity due to closure decisions and repair procedures. This data is utilized to assess the probability of meeting various damage states, expressed in terms of restoration of functionality, and subsequently facilitate the refinement of component limit-state capacities for analytical fragility curve development. The bridge functionality relationships and methodology outlined serve as the basis for refinement of critical tools in the seismic risk assessment framework and improved assessment of transportation network performance.
Memento’s Revenge: The Extended Mind, Extended

In the movie, Memento, the hero, Leonard, suffers from a form of anterograde amnesia that results in an inability to lay down new memories. Nonetheless, he sets out on a quest to find his wife’s killer, aided by the use of notes, annotated polaroids, and (for the most important pieces of information obtained) body tattoos. Using these resources he attempts to build up a stock of new beliefs and to thus piece together the puzzle of his wife’s death. At one point in the movie, a character exasperated by Leonard’s lack of biological recall, shouts:
Alcohol‐responsive genes in the frontal cortex and nucleus accumbens of human alcoholics

The molecular processes underlying alcohol dependence are not fully understood. Many characteristic behaviours result from neuroadaptations in the mesocorticolimbic system. In addition, alcoholism is associated with a distinct neuropathology. To elucidate the molecular basis of these features, we compared the RNA expression profile of the nucleus accumbens and prefrontal cortex of human brain from matched individual alcoholic and control cases using cDNA microarrays. Approximately 6% of genes with a marked alcohol response were common to the two brain regions. Alcohol-responsive genes were grouped into 11 functional categories. Predominant alcohol-responsive genes in the prefrontal cortex were those encoding DNA-binding proteins including transcription factors and repair proteins. There was also a down-regulation of genes encoding mitochondrial proteins, which could result in disrupted mitochondrial function and energy production leading to oxidative stress. Other alcohol-responsive genes in the prefrontal cortex were associated with neuroprotection/apoptosis. In contrast, in the nucleus accumbens, alcohol-responsive genes were associated with vesicle formation and regulation of cell architecture, which suggests a neuroadaptation to chronic alcohol exposure at the level of synaptic structure and function. Our data are in keeping with the previously reported alcoholism-related pathology characteristic of the prefrontal cortex, but suggest a persistent decrease in neurotransmission and changes in plasticity in the nucleus accumbens of the alcoholic.
Association of Variants at UMOD with Chronic Kidney Disease and Kidney Stones—Role of Age and Comorbid Diseases

Chronic kidney disease (CKD) is a worldwide public health problem that is associated with substantial morbidity and mortality. To search for sequence variants that associate with CKD, we conducted a genome-wide association study (GWAS) that included a total of 3,203 Icelandic cases and 38,782 controls. We observed an association between CKD and a variant with 80% population frequency, rs4293393-T, positioned next to the UMOD gene (GeneID: 7369) on chromosome 16p12 (OR = 1.25, P = 4.1×10−10). This gene encodes uromodulin (Tamm-Horsfall protein), the most abundant protein in mammalian urine. The variant also associates significantly with serum creatinine concentration (SCr) in Icelandic subjects (N = 24,635, P = 1.3×10−23) but not in a smaller set of healthy Dutch controls (N = 1,819, P = 0.39). Our findings validate the association between the UMOD variant and both CKD and SCr recently discovered in a large GWAS. In the Icelandic dataset, we demonstrate that the effect on SCr increases substantially with both age (P = 3.0×10−17) and number of comorbid diseases (P = 0.008). The association with CKD is also stronger in the older age groups. These results suggest that the UMOD variant may influence the adaptation of the kidney to age-related risk factors of kidney disease such as hypertension and diabetes. The variant also associates with serum urea (P = 1.0×10−6), uric acid (P = 0.0064), and suggestively with gout. In contrast to CKD, the UMOD variant confers protection against kidney stones when studied in 3,617 Icelandic and Dutch kidney stone cases and 43,201 controls (OR = 0.88, P = 5.7×10−5).