Miracle-dz/UniFAR-FTUs huggingface dataset:
Icariin promotes stable chondrogenic differentiation of bone marrow mesenchymal stem cells in self-assembling peptide nanofiber hydrogel scaffolds

Icariin, a traditional Chinese medicine, has previously been demonstrated to promote chondrogenesis of bone marrow mesenchymal stem cells (BMSCs) in traditional 2D cell culture. The present study investigated whether icariin has the potential to promote stable chondrogenic differentiation of BMSCs without hypertrophy in a 3D microenvironment. BMSCs were cultivated in a self-assembling peptide nanofiber hydrogel scaffold in chondrogenic medium for 3 weeks. Icariin was added to the medium throughout the culture period at concentrations of 1×10−6 M. Chondrogenic differentiation markers, including collagen II and SRY-type high mobility group box 9 (SOX9) were detected by immunofluorescence, reverse transcription-quantitative polymerase chain reaction and toluidine blue staining. Hypertrophic differentiation was further assessed by detecting collagen X and collagen I gene expression levels and alkaline phosphatase activity. The results demonstrated that icariin significantly enhanced cartilage extracellular matrix synthesis and gene expression levels of collagen II and SOX9, and additionally promoted more chondrocyte-like rounded morphology in BMSCs. Furthermore, chondrogenic medium led to hypertrophic differentiation via upregulation of collagen X and collagen I gene expression levels and alkaline phosphatase activity, which was not potentiated by icariin. In conclusion, these results suggested that icariin treatment may promote chondrogenic differentiation of BMSCs, and inhibit the side effect of growth factor activity, thus preventing further hypertrophic differentiation. Therefore, icariin may be a potential compound for cartilage tissue engineering.
A survey of computational molecular science using graphics processing units

Computational molecular science is a very computationally intense discipline, and the use of parallel programming and high‐performance computers well established as being necessary to support research activities. Recently, graphical processing units (GPUs) have garnered substantial interest as alternative sources of high‐performance computing capability. These devices, although capable of very high rates of floating‐point arithmetic, are also intrinsically highly parallel processors and their effective exploitation typically requires extensive software refactoring and development. Here, we review the current landscape of GPU hardware and programming models, and provide a snapshot survey of the current state of computational molecular science codes ported to GPUs to help domain scientists and software developers understand the potential benefits and drawbacks of this new computing architecture. © 2012 John Wiley & Sons, Ltd.
Dynamic deformation of solid primitives with constraints

This paper develops a systematic approach to deriving dynamic models from parametrically defined solid primitives, global geometric deformations and local finite- element deformations. Even though their kinematics is styl- ized by the particular solid primitive used, the models be- have in a physically correct way with prescribed mass dis- tributions and elasticities. We also propose efficient con- straint methods for connecting these new dynamic primitives together to make articulated models. Our techniques make it possible to build and animate constrained, nonrigid, unibody or multibody objects in simulated physical environments at interactive rates. 1 Introduction The graphics literature is replete with solid object representa- tions. Unfortunately, it is not particularly easy to synthesize realistic animation through direct application of the geomet- ric representations of solid modeling (5), and the problems are exacerbated when animate objects can deform. Physics- based animation has begun to overcome some of the difficul- ties. We propose a systematic approach for creating dynamic solid models capable of realistic physical behaviors starting from common solid primitives such as spheres, cylinders, cones, or superquadrics. Such primitives can "deform" kine- matically in simple ways; for example, a cylinder deforms as its radius or length is changed. To gain additional model- ing power we allow the primitives to undergo parameterized global deformations (bends, tapers, twists, shears, etc.) of the sort proposed in (2). To further enhance the geometric flexibility, we permit local free-form deformations. Our lo- cal deformations are similar in spirit to the FFDs of (12), but rather than being ambient space warps (12, 10), they are in- corporated directly into the solid primitive as finite element shape functions. Through the application of Lagrangian mechanics and the finite element method our models inherit generalized coor- dinates that comprise the geometric parameters of the solid primitive, the global and local deformation parameters, and the six degrees of freedom of rigid-body motion. Lagrange equations govern the dynamics, dictating the evolution of the
era of patients with recurrent miscarriages containing nti-trophoblast antibodies ( ATAB ) reduce hCG and progesterone roduction in trophoblast cells in vitro iktoria

Problem: Reproductive failure including RM has been suggested to correlate with antibodies that cross react with HLA-negative syncytiotrophoblasts and we have reported that 17% of women with 2 or more miscarriages and 34% of women with 3 or more miscarriages express anti-trophoblast antibodies (ATAB). Until now, the mechanism, how ATAB interfere with pregnancy success is not known. HCG and progesterone both play fundamental roles in supporting human pregnancy. Therefore we investigated the effects of sera of RM patients containing ATAB on the hCG and progesterone production of cells of the choriocarcinoma cell line JEG-3. Method of study: In vitro study to investigate effects of patient sera with and without ATAB on hCG and progesterone secretion of JEG-3 cells. The presence of ATAB was detected as described earlier. Effects of sera from ATAB positive and ATAB negative RM patients on hCG and progesterone secretion by JEG-3 cells were analysed 12 and 24 h after plating. Sera of women without pregnancy pathologies served as controls. Results: Sera of ATAB-positive RM patients significantly inhibit hCG secretion of JEG-3 cells for 12 h after plating compared to sera of healthy controls (p = 0.019) and significantly reduce progesterone production for 12 h (p = 0.046) and 24 h (p = 0.027) of co-culture. Sera of ATAB-negative RM patient show no significant effect on progesterone secretion. Conclusions: Inhibition of hCG and progesterone production might point to a mechanism, how ATAB interfere with early pregnancies. © 2016 Elsevier Ireland Ltd. All rights reserved.
Molecular principles of hair follicle induction and morphogenesis

Hair follicle (HF) development is the result of neuroectodermal–mesodermal interactions, and can be divided into morphologically distinguishable stages (induction, organogenesis and cytodifferentiation). The spacing, polarity and differentiation patterns of HFs are driven by interacting, self‐assembling gradients of inhibitors and activators, which are established jointly by the skin epithelium and mesenchyme. For HF development to occur, the dominant‐negative influence of inhibitors of the HF differentiation pathway must be locally counteracted by specific antagonists and/or overriden by stimulators of hair placode formation. Once a mesenchymal condensate of inductive fibroblasts has formed, it takes over control of most subsequent steps of HF organogenesis and of epithelial stem cell differentiation into distinct lineages. In this review we introduce the morphological characteristics, major underlying principles and molecular key players that control HF development. The focus is on recent insights into the molecular interactions leading to hair follicle induction, and we close with synthesizing a corresponding working hypothesis. BioEssays 27:247–261, 2005. © 2005 Wiley Periodicals, Inc.
Twitter and Urdu

The modern social media is generating terabytes of data in AVT (audio, video and text) format, which mainly comprises of opinions, relations or expressions. Language has always been a way of communication and interaction primarily used in the form of words or signs. Humans have used verbal and physical expression to convey their feelings to facilitate communication. ‘Urdu’ is the national language of Pakistan and has evolved from several languages; such as Persian, Arabic, Hindi, Sanskrit and Prakrit dating back to the 6th to 13th Century. This study will use the Twitter handle for social media applications sample data to analyze and derive the Urdu language and see the status of Urdu language communication using Twitter. The biggest challenge of this study is that Urdu communication occurs in the form of traditional Urdu and roman Urdu, which makes identification of tweet corpse difficult.
Joint Testlet Cognitive Diagnosis Modeling for Paired Local Item Dependence in Response Times and Response Accuracy

In joint models for item response times (RTs) and response accuracy (RA), local item dependence is composed of local RA dependence and local RT dependence. The two components are usually caused by the same common stimulus and emerge as pairs. Thus, the violation of local item independence in the joint models is called paired local item dependence. To address the issue of paired local item dependence while applying the joint cognitive diagnosis models (CDMs), this study proposed a joint testlet cognitive diagnosis modeling approach. The proposed approach is an extension of Zhan et al. (2017) and it incorporates two types of random testlet effect parameters (one for RA and the other for RTs) to account for paired local item dependence. The model parameters were estimated using the full Bayesian Markov chain Monte Carlo (MCMC) method. The 2015 PISA computer-based mathematics data were analyzed to demonstrate the application of the proposed model. Further, a brief simulation study was conducted to demonstrate the acceptable parameter recovery and the consequence of ignoring paired local item dependence.
Atmospheric deposition of reactive nitrogen oxides and ozone in a temperate deciduous forest and a subarctic woodland

We present 5 years of NOy and 0 3 eddy flux and concentration measurements and NO x concentration measurements at Harvard Forest (1990-1994), a mixed deciduous forest in cen- tral Massachusetts, and 2 months of data for a spruce woodland near Schefferville, Quebec, during the NASA ABLE3B/Northem Wetlands Study (1990). Mean midday values of net dry NOy flux from atmosphere to canopy were 3.4 and 3.2 gmole m -2 hr-1 at Harvard Forest in summer and 2 winter, respectively, and 0.5 (tmole m- hr- at Schefferville during summer. Nighttime values were 2 1 1.3, 2.0, and 0.15 tmole m- hr- , respectively. For 1990-1994, the net annual dry deposition of 2 1 1 1 nitrogen oxides was 17.9 mmole rn- yr- (2.49 kgN ha- y- ). Oxidized species such as HNO 3 dominated N deposition, with minor contributions from direct deposition of NO 2. Emissions of NO from the forest soil were negligible compared to deposition. Comparison of NOy deposition at Harvard Forest and Schefferville and analysis of the dependence on meteorological parameters show that anthropogenic sources dominate the nitrogen oxide inputs over much of North America. Heterogeneous reactions account for >90% of the conversion of NO 2 to HNO 3 in winter, leading to rates for dry deposition of NOy similar to fluxes in summer despite 10-fold decrease in OH con- centrations. In summer, formation of HNO 3 by heterogeneous reactions (mainly at night) could provide 25-45% of the NO2 oxidation.
Improving Policing: A Problem-Oriented Approach

The police have been particularly susceptible to the "means over ends" syndrome, placing more emphasis in their improvement efforts on organization and operating methods than on the substantive outcome of their work. This condition has been fed by the professional movement within the police field, with its concentration on the staffing, management, and organization of police agencies. More and more persons are questioning the widely held assumption that improvements in the internal man agement of police departments will enable the police to deal more effectively with the problems they are called upon to handle. If the police are to realize a greater return on the investment made in improving their oper ations, and if they are to mature as a profession, they must concern them selves more directly with the end product of their efforts.
Gender Differences in Intimate Partner Violence and Subsequent Arrests: An Analysis of Police Reports in a Small Western City

Although a significant amount of literature addresses the perpetration of intimate partner violence (IPV), there are conflicting results about how gender is related to offending and victimization, and there is no universally accepted model with which to analyze IPV incidents. In the same vein, there are questions about how police officers and other legal system actors should respond to IPV and whether current policies are effective in protecting victims and reducing recidivism. The aim of this study is to conduct a gendered analysis of IPV arrests in a small Western city, both in terms of the identified arrestees’ and complainants’ gender and the arresting police officers’ gender. A sample of 100 IPV-related arrest reports filed in a small Western city was coded both quantitatively and qualitatively to document how gender affects domestic violence (DV) arrests. In general, the results of this study support feminist views that IPV is gendered, but is also consistent with the family violence scholars given the numerous similarities that also exist between genders in the victimization and offending results. Additionally, the findings demonstrate arrestee differences based on both race/ethnicity and sexual orientation. Specifically, they suggest that among those arrested for DV, women are more likely than men to be in same-sex relationships, and Latino and African-American men are more likely to be arrested than White men. Importantly, the analysis also reveals inadequacy of officer recognition of mental health problems. Few differences in officer gender were found regarding these arrests. Finally, implications and suggestions for future direction are examined.
What do we know about the defect types detected in conceptual models?

In Model-Driven Development (MDD), defects are managed at the level of conceptual models because the other artefacts are generated from them, such as more refined models, test cases and code. Although some studies have reported on defect types at model level, there still does not exist a clear and complete overview of the defect types that occur at the abstraction level. This paper presents a systematic mapping study to identify the model defect types reported in the literature and determine how they have been detected. Among the 282 articles published in software engineering area, 28 articles were selected for analysis. A total of 226 defects were identified, classified and their results analysed. For this, an appropriate defect classification scheme was built based on appropriate dimensions for models in an MDD context.
Regulation of Rat Liver Epoxide Hydrolase by Tightly Bound Phosphoinositides

Rat liver microsomal epoxide hydrolase (styrene oxide hydrolase) has three tightly bound phosphoinositides in its native state. Two methods of purification yielded an enzyme with apparent homogeneity. When dried films of this enzyme were repeatedly extracted with chloroform/methanol, the lipid-free films still contained bound inositides. Further extraction of the enzyme film using acidified chloroform/methanol gave three phosphoinositides per enzyme of 50,000 Da. Thin layer chromatography of the protein-bound inositides showed two to be phosphatidyl inositol and one to be phosphatidyl inositol 4-phosphate. Physical and chemical evidence suggests covalent binding between inositides and enzyme. After incubation at pH 9.2 for 16 hr at 4°C followed by chromatofocusing, an inositide-free, active enzyme was obtained. This inositide-free enzyme had much higher epoxide hydrolase activity than the inositide-bound enzyme. The enzyme activity was not inhibited by the presence of phosphatidyl inositol and phosphatidyl inositol 4-phosphate. These results suggest that the attachment of inositides is critical for the difference in styrene oxide hydrolase activity in low-ionic strength buffer between the native, inositide-containing enzyme (low activity) and the inositide-free enzyme (higher activity). ©1999 Oklahoma Academy of Science
STAT3 Expression, Molecular Features, Inflammation Patterns, and Prognosis in a Database of 724 Colorectal Cancers

Purpose: STAT3 is a transcription factor that is constitutively activated in some cancers. It seems to play crucial roles in cell proliferation and survival, angiogenesis, tumor-promoting inflammation, and suppression of antitumor host immune response in the tumor microenvironment. Although the STAT3 signaling pathway is a potential drug target, clinical, pathologic, molecular, or prognostic features of STAT3-activated colorectal cancer remain uncertain. Experimental Design: Utilizing a database of 724 colon and rectal cancer cases, we evaluated phosphorylated STAT3 (p-STAT3) expression by immunohistochemistry. The Cox proportional hazards model was used to compute mortality HR, adjusting for clinical, pathologic, and molecular features, including microsatellite instability (MSI), the CpG island methylator phenotype (CIMP), LINE-1 methylation, 18q LOH, TP53 (p53), CTNNB1 (β-catenin), JC virus T-antigen, and KRAS, BRAF, and PIK3CA mutations. Results: Among the 724 tumors, 131 (18%) showed high-level p-STAT3 expression (p-STAT3-high), 244 (34%) showed low-level expression (p-STAT3-low), and the remaining 349 (48%) were negative for p-STAT3. p-STAT3 overexpression was associated with significantly higher colorectal cancer–specific mortality [log-rank P = 0.0020; univariate HR (p-STAT3-high vs. p-STAT3-negative): 1.85, 95% CI: 1.30–2.63, Ptrend = 0.0005; multivariate HR: 1.61, 95% CI: 1.11–2.34, Ptrend = 0.015]. p-STAT3 expression was positively associated with peritumoral lymphocytic reaction (multivariate OR: 3.23; 95% CI: 1.89–5.53, P < 0.0001). p-STAT3 expression was not associated with MSI, CIMP, or LINE-1 hypomethylation. Conclusions: STAT3 activation in colorectal cancer is associated with adverse clinical outcome, supporting its potential roles as a prognostic biomarker and a chemoprevention and/or therapeutic target. Clin Cancer Res; 17(6); 1452–62. ©2011 AACR.
The neurobiology of aggression and violence

Aggression and violence represent a significant public health concern and a clinical challenge for the mental healthcare provider. A great deal has been revealed regarding the neurobiology of violence and aggression, and an integration of this body of knowledge will ultimately serve to advance clinical diagnostics and therapeutic interventions. We will review here the latest findings regarding the neurobiology of aggression and violence. First, we will introduce the construct of aggression, with a focus on issues related to its heterogeneity, as well as the importance of refining the aggression phenotype in order to reduce pathophysiologic variability. Next we will examine the neuroanatomy of aggression and violence, focusing on regional volumes, functional studies, and interregional connectivity. Significant emphasis will be on the amygdala, as well as amygdala–frontal circuitry. Then we will turn our attention to the neurochemistry and molecular genetics of aggression and violence, examining the extensive findings on the serotonergic system, as well as the growing literature on the dopaminergic and vasopressinergic systems. We will also address the contribution of steroid hormones, namely, cortisol and testosterone. Finally, we will summarize these findings with a focus on reconciling inconsistencies and potential clinical implications; and, then we will suggest areas of focus for future directions in the field.
Experimental study on the influence of the sensor and actuator arrangement on the performance of an active noise blocker for a tilted window

Closed windows reduce noise by approximately 20 dB. Unfortunately, they block fresh air circulation at the same time. To solve this problem, an active noise blocker (ANB) has been set up. It consists of a set of microphones and loudspeakers driven by a MIMO FxLMS (multiple input multiple output filtered reference (x) least mean square) controller on the real time processor. The goal of the ANB is to generate sound pressure nodes to stop the transfer of acoustic energy into the room, using a low but sufficient number of secondary loudspeakers placed in the transmission path. This specific local anti-noise measure shall achieve a high global noise reduction inside the room. Preceding numerical studies have shown, that the arrangement of the sensors and actuators of the ANB in the transmission path has significant effect on its performance. This study checks experimentally different combinations of the setup of the system components with regard to their influence on the performance of the ANB. Additionally this study includes the realization of an add-on kit for an already installed window.
Response by Wong et al to Letter Regarding Article, "Importance of Routine Antihuman/Leukocyte Antibody Monitoring: De Novo Donor Specific Antibodies Are Associated With Rejection and Allograft Vasculopathy After Heart Transplantation".

We thank Clerkin et al for their interest in our study addressing the importance of routine monitoring for de novo donor–specific antibodies (dnDSA) not only in predicting cellular and antibody-mediated rejection (AMR) but also for the first time demonstrating its association with allograft vasculopathy detected by intravascular ultrasound.1 Our data were analyzed using a Cox regression survival analysis model accounting for the timing of dnDSA events when predicting subsequent incidence of AMR. In 2 previous studies cited by Clerkin, patients at time of transplant were classified according to posttransplant outcomes such as dnDSA or AMR. Statistical theory does not …
Sir David Cuthbertson Medal Lecture Bariatric surgery as a model to study appetite control

The obesity epidemic and its associated morbidity and mortality have led to major research efforts to identify mechanisms that regulate appetite. Gut hormones have recently been found to be an important element in appetite regulation as a result of the signals from the periphery to the brain. Candidate hormones include ghrelin, peptide YY, glucagon-like peptide-1 and gastric inhibitory polypeptide, all of which are currently being investigated as potential obesity treatments. Bariatric surgery is currently the most effective therapy for substantial and sustained weight loss. Understanding how levels of gut hormones are modulated by such procedures has greatly contributed to the comprehension of the underlying mechanisms of appetite and obesity. The present paper is a review of how appetite and levels of gastrointestinal hormones are altered after bariatric surgery. Basic principles of common bariatric procedures and potential mechanisms for appetite regulation by gut hormones are also addressed.