Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface topography during neural stem cell differentiation regulates cell migration and cell morphology

We sought to determine the contribution of scaffold topography to the migration and morphology of neural stem cells by mimicking anatomical features of scaffolds found in vivo. We mimicked two types of central nervous system scaffolds encountered by neural stem cells during development in vitro by constructing different diameter electrospun polycaprolactone (PCL) fiber mats, a substrate that we have shown to be topographically similar to brain scaffolds. We compared the effects of large fibers (made to mimic blood vessel topography) with those of small‐diameter fibers (made to mimic radial glial process topography) on the migration and differentiation of neural stem cells. Neural stem cells showed differential migratory and morphological reactions with laminin in different topographical contexts. We demonstrate, for the first time, that neural stem cell biological responses to laminin are dependent on topographical context. Large‐fiber topography without laminin prevented cell migration, which was partially reversed by treatment with rock inhibitor. Cell morphology complexity assayed by fractal dimension was inhibited in nocodazole‐ and cytochalasin‐D–treated neural precursor cells in large‐fiber topography, but was not changed in small‐fiber topography with these inhibitors. These data indicate that cell morphology has different requirements on cytoskeletal proteins dependent on the topographical environment encountered by the cell. We propose that the physical structure of distinct scaffolds induces unique signaling cascades that regulate migration and morphology in embryonic neural precursor cells. J. Comp. Neurol. 524:3485–3502, 2016. © 2016 Wiley Periodicals, Inc.
Applying Machine Learning to Predict and Explain Primate Consortship

We apply machine learning methods to investigate the behavioral and genetic reasons for success and failure of mating between wild baboon pairs. The mating behavior of a species drives genetic interchange and is a major driver of evolution within populations. Factors that contribute to consortship may range from genetic causes, such as physical traits expressed due to the presence of a gene, to those that are social or behavioral. The contribution of social factors is of particular interest for animals that live in structured groups, where factors such as rank within a social heirarchy may impact mating success. Investigating this topic will provide deeper insight into the factors of mating success in social mammals, which may be extended to apply to humans as well.
Towards a stakeholder analysis of information systems development project abandonment

This study adopts a stakeholder analysis to examine stakeholders’ roles and contributions in influencing organizational decisions to abandon information systems (IS) development projects. To do so, we adapted from Freeman’s (1984) work and developed a theoretical assessment framework to organize and interpret data, and define avenues (five propositions were proposed) for further research into IS project abandonment. By providing a better understanding of the project stakeholders’ perception, expectations and their interrelationship, this study provides practitioners with useful insights on how to manage stakeholders in IS development projects. Our contribution lies in the development of a project abandonment review model that adds a stakeholder perspective.
Using Transmural Regularization and Dynamic Modeling for Noninvasive Cardiac Potential Imaging of Endocardial Pacing With Imprecise Thoracic Geometry

Cardiac electrical imaging from body surface potential measurements is increasingly being seen as a technology with the potential for use in the clinic, for example for pre-procedure planning or during-treatment guidance for ventricular arrhythmia ablation procedures. However several important impediments to widespread adoption of this technology remain to be effectively overcome. Here we address two of these impediments: the difficulty of reconstructing electric potentials on the inner (endocardial) as well as outer (epicardial) surfaces of the ventricles, and the need for full anatomical imaging of the subject's thorax to build an accurate subject-specific geometry. We introduce two new features in our reconstruction algorithm: a nonlinear low-order dynamic parameterization derived from the measured body surface signals, and a technique to jointly regularize both surfaces. With these methodological innovations in combination, it is possible to reconstruct endocardial activation from clinically acquired measurements with an imprecise thorax geometry. In particular we test the method using body surface potentials acquired from three subjects during clinical procedures where the subjects' hearts were paced on their endocardia using a catheter device. Our geometric models were constructed using a set of CT scans limited in axial extent to the immediate region near the heart. The catheter system provides a reference location to which we compare our results. We compare our estimates of pacing site localization, in terms of both accuracy and stability, to those reported in a recent clinical publication , where a full set of CT scans were available and only epicardial potentials were reconstructed.
Analyzing Networks of Issue Reports

Completely analyzed and closed issue reports in software development projects, particularly in the development of safety-critical systems, often carry important information about issue-related change locations. These locations may be in the source code, as well as traces to test cases affected by the issue, and related design and requirements documents. In order to help developers analyze new issues, knowledge about issue clones and duplicates, as well as other relations between the new issue and existing issue reports would be useful. This paper analyses, in an exploratory study, issue reports contained in two Issue Management Systems (IMS) containing approximately 20.000 issue reports. The purpose of the analysis is to gain a better understanding of relationships between issue reports in IMSs. We found that link-mining explicit references can reveal complex networks of issue reports. Furthermore, we found that textual similarity analysis might have the potential to complement the explicitly signaled links by recommending additional relations. In line with work in other fields, links between software artifacts have a potential to improve search and navigation in large software engineering projects.
Dynamic cultivation of human mesenchymal stem cells in a rotating bed bioreactor system based on the Z®RP platform

Because the regeneration of large bone defects is limited by quantitative restrictions and risks of infections, the development of bioartificial bone substitutes is of great importance. To obtain a three‐dimensional functional tissue‐like graft, static cultivation is inexpedient due to limitations in cell density, nutrition and oxygen support. Dynamic cultivation in a bioreactor system can overcome these restrictions and furthermore provide the possibility to control the environment with regard to pH, oxygen content, and temperature. In this study, a three‐dimensional bone construct was engineered by the use of dynamic bioreactor technology. Human adipose tissue derived mesenchymal stem cells were cultivated on a macroporous zirconium dioxide based ceramic disc called Sponceram®. Furthermore, hydroxyapatite coated Sponceram® was used. The cells were cultivated under dynamic conditions and compared with statically cultivated cells. The differentiation into osteoblasts was initiated by osteogenic supplements. Cellular proliferation during static and dynamic cultivation was compared measuring glucose and lactate concentration. The differentiation process was analysed determining AP‐expression and using different specific staining methods. Our results demonstrate much higher proliferation rates during dynamic conditions in the bioreactor system compared to static cultivation measured by glucose consumption and lactate production. Cell densities on the scaffolds indicated higher proliferation on native Sponceram® compared to hydroxyapatite coated Sponceram®. With this study, we present an excellent method to enhance cellular proliferation and bone lineage specific growth of tissue like structures comprising fibrous (collagen) and globular (mineral) extracellular components. © 2009 American Institute of Chemical Engineers Biotechnol. Prog. , 2009
Evaluating TMPA Rainfall over the Sparsely Gauged East African Rift

Accurate precipitation data are fundamental for understanding and mitigating the disastrous effects of many natural hazards in mountainous areas. Floods and landslides, in particular, are potentially deadly events that can be mitigated with advanced warning, but accurate forecasts require timely estimation of precipitation, which is problematic in regions such as tropical Africa with limited gauge measurements. Satellite rainfall estimates (SREs) are of great value in such areas, but rigorous validation is required to identify the uncertainties linked to SREs for hazard applications. This paper presents results of an unprecedented record of gauge data in the western branch of the East African Rift, with temporal resolutions ranging from 30 min to 24 h and records from 1998 to 2018. These data were used to validate the Tropical Rainfall Measuring Mission (TRMM) Multisatellite Precipitation Analysis (TMPA) research version and near-real-time products for 3-hourly, daily, and monthly rainfall accumulations, over multiple spatial scales. Results indicate that there are at least two factors that led to the underestimation of TMPA at the regional level: complex topography and high rainfall intensities. The TMPA near-real-time product shows overall stronger rainfall underestimations but lower absolute errors and a better performance at higher rainfall intensities compared to the research version. We found area-averaged TMPA rainfall estimates relatively more suitable in order to move toward regional hazard assessment, compared to data from scarcely distributed gauges with limited representativeness in the context of high rainfall variability.
Image quality validation of Sentinel 2 Level-1 products: performance status at the beginning of the constellation routine phase

Sentinel-2 is an Earth Observation mission developed by the European Space Agency (ESA) in the frame of the Copernicus program of the European Commission. The mission is based on a constellation of 2-satellites: Sentinel-2A launched in June 2015 and Sentinel-2B launched in March 2017. It offers an unprecedented combination of systematic global coverage of land and coastal areas, a high revisit of five days at the equator and 2 days at mid-latitudes under the same viewing conditions, high spatial resolution, and a wide field of view for multispectral observations from 13 bands in the visible, near infrared and short wave infrared range of the electromagnetic spectrum. The mission performances are routinely and closely monitored by the S2 Mission Performance Centre (MPC), including a consortium of Expert Support Laboratories (ESL). This publication focuses on the Sentinel-2 Level-1 product quality validation activities performed by the MPC. It presents an up-to-date status of the Level-1 mission performances at the beginning of the constellation routine phase. Level-1 performance validations routinely performed cover Level-1 Radiometric Validation (Equalisation Validation, Absolute Radiometry Vicarious Validation, Absolute Radiometry Cross-Mission Validation, Multi-temporal Relative Radiometry Vicarious Validation and SNR Validation), and Level-1 Geometric Validation (Geolocation Uncertainty Validation, Multi-spectral Registration Uncertainty Validation and Multi-temporal Registration Uncertainty Validation). Overall, the Sentinel-2 mission is proving very successful in terms of product quality thereby fulfilling the promises of the Copernicus program.
General Considerations

Drug interaction, modification of the effects of one drug by another, is a serious problem. This series of articles will deal with the interaction of drugs with other chemical agents, both exogenous and endogenous, as well as those found in foods and those utilized in diagnostic tests. To understand drug interactions and their significance, one must be familiar with the terminology, with the biological sciences, clinical use of drugs, and the current pharmaco-medical literature.
Pediatricians' practices and attitudes regarding breastfeeding promotion.

OBJECTIVE Public awareness of the benefits of breastfeeding is expected to increase during and after the national, federally funded Best Start Breastfeeding Promotion Campaign. It is anticipated that this will result in more breastfeeding-based interactions between families and pediatricians. The American Academy of Pediatrics conducted a survey of its members to identify their educational needs regarding breastfeeding to assist in the design of appropriate information programs. METHOD An eight-page, self-administered questionnaire was sent to 1602 active Fellows of the American Academy of Pediatrics. RESULTS The response rate was 71%. Breastfeeding, as the exclusive feeding practice for the first month after birth, was recommended by only 65% of responding pediatricians; only 37% recommended breastfeeding for 1 year. A majority of pediatricians agreed with or had a neutral opinion about the statement that breastfeeding and formula-feeding are equally acceptable methods for feeding infants. Reasons given for not recommending breastfeeding included medical conditions with known treatments that did not preclude breastfeeding. The majority of pediatricians (72%) were unfamiliar with the contents of the Baby-Friendly Hospital Initiative. The majority of pediatricians had not attended a presentation on breastfeeding management in the previous 3 years; most said they wanted more education on breastfeeding management. CONCLUSION Pediatricians have significant educational needs in the area of breastfeeding management.
Optimal Content Placement for Peer-to-Peer Video-on-Demand Systems

In this paper, we address the problem of content placement in peer-to-peer (P2P) systems, with the objective of maximizing the utilization of peers' uplink bandwidth resources. We consider system performance under a many-user asymptotic. We distinguish two scenarios, namely “Distributed Server Networks” (DSNs) for which requests are exogenous to the system, and “Pure P2P Networks” (PP2PNs) for which requests emanate from the peers themselves. For both scenarios, we consider a loss network model of performance and determine asymptotically optimal content placement strategies in the case of a limited content catalog. We then turn to an alternative “large catalog” scaling where the catalog size scales with the peer population. Under this scaling, we establish that storage space per peer must necessarily grow unboundedly if bandwidth utilization is to be maximized. Relating the system performance to properties of a specific random graph model, we then identify a content placement strategy and a request acceptance policy that jointly maximize bandwidth utilization, provided storage space per peer grows unboundedly, although arbitrarily slowly, with system size.
Dissemination patterns in non-gastric MALT lymphoma

Primary extranodal non-gastric marginal zone MALT lymphoma frequently present with stage IV disease and multifocal disease, and a site-specific dissemination pattern. Extensive staging at diagnosis of fundamental importance. Background In contrast to gastric extranodal marginal zone mucosa associated lymphoid tissue (MALT) lymphomas, there is little consensus on the value and clinical consequences of extensive staging at diagnosis and during follow-up in non-gastric MALT lymphomas. Design and Methods Complete clinical information at presentation and during follow-up was collected for 72 patients with non-gastric MALT lymphoma treated at the Netherlands Cancer Institute between 1977 and 2005. Dissemination patterns at presentation were studied for nine primary dominant organ groups in our series of 72 patients and in a similar cohort treated at Vienna University (for a total of 106 patients). Results Twenty-three of our patients (32%) had more than one site of extranodal MALT lymphomatous disease, 13 patients (18%) had regional nodal involvement and 7 (10%) had bone marrow involvement. Site-specific dissemination was seen in paired organs (orbit, lung) and in the gastrointestinal tract (stomach, colon) and primary pulmonary MALT lymphoma was specifically related to gastric involvement (p<0.0001). These patterns of dissemination were retained during relapsed disease. Conclusions Primary extranodal non-gastric marginal zone MALT lymphoma frequently presents as stage IV disease (26%) and multifocal disease (32%) and with a site-specific dissemination pattern. After an extensive staging procedure at presentation, we recommend primary site-directed protocols during follow-up focused on the primary involved tract/organ system, regional lymph nodes and pulmonary and gastric relapses.
On the distribution of DNA translocation times in solid-state nanopores: an analysis using Schrödinger’s first-passage-time theory

In this short paper, a correction is made to the recently proposed solution of Li and Talaga to a 1D biased diffusion model for linear DNA translocation, and a new analysis will be given to their data. It was pointed out by us recently that this 1D linear translocation model is equivalent to the one that was considered by Schrödinger for the Ehrenhaft–Millikan measurements on electron charge. Here, we apply Schrödinger’s first-passage-time distribution formula to the data set in Li and Talaga. It is found that Schrödinger’s formula can be used to describe the time distribution of DNA translocation in solid-state nanopores. These fittings yield two useful parameters: the drift velocity of DNA translocation and the diffusion constant of DNA inside the nanopore. The results suggest two regimes of DNA translocation: (I) at low voltages, there are clear deviations from Smoluchowski’s linear law of electrophoresis, which we attribute to the entropic barrier effects; (II) at high voltages, the translocation velocity is a linear function of the applied electric field. In regime II, the apparent diffusion constant exhibits a quadratic dependence on the applied electric field, suggesting a mechanism of Taylor-dispersion effect likely due the electro-osmotic flow field in the nanopore channel. This analysis yields a dispersion-free diffusion constant value of 11.2 nm2 μs−1 for the segment of DNA inside the nanopore, which is in quantitative agreement with the Stokes–Einstein theory. The implication of Schrödinger’s formula for DNA sequencing is discussed.
Prior statin use, intracranial hemorrhage, and outcome after intra-arterial thrombolysis for acute ischemic stroke.

BACKGROUND AND PURPOSE There are only limited data on whether prior statin use and/or cholesterol levels are associated with intracranial hemorrhage (ICH) and outcome after intra-arterial thrombolysis. The purpose of this study was to evaluate the association of statin pretreatment and cholesterol levels with the overall frequency of ICH, the frequency of symptomatic ICH, and clinical outcome at 3 months. METHODS We analyzed 311 consecutive patients (mean age, 63 years; 43% women) who received intra-arterial thrombolysis. RESULTS Statin pretreatment was present in 18%. The frequency of any ICH was 20.6% and of symptomatic ICH 4.8%. Patients with any ICH were more often taking statins (30% versus 15%, P=0.005), more often had atrial fibrillation (45% versus 30%, P=0.016), had more severe strokes (mean National Institute of Health Stroke Scale score 16.5 versus 14.7, P=0.022), and less often good collaterals (16% versus 24%, P=0.001). Patients with symptomatic ICH were more often taking statins (40% versus 15%, P=0.009) and had less often good collaterals (0% versus 24%, P<0.001). Any ICH or symptomatic ICH were not associated with cholesterol levels. After multivariate analysis, the frequency of any ICH remained independently associated with previous statin use (OR, 3.1; 95% CI, 1.53 to 6.39; P=0.004), atrial fibrillation (OR, 2.5; CI, 1.35 to 4.75; P=0.004), National Institutes of Health Stroke Scale score (OR, 1.1; CI, 1.00 to 1.10; P=0.037), and worse collaterals (OR, 1.7; CI, 1.19 to 2.42; P=0.004). There was no association of outcome with prior statin use, total cholesterol level, or low-density lipoprotein cholesterol level. CONCLUSIONS Prior statin use, but not cholesterol levels on admission, is associated with a higher frequency of any ICH after intra-arterial thrombolysis without impact on outcome.
Masculinized Sexual Partner Preference in Female Zebra Finches with Sex-Reversed Gonads

Previous research in the zebra finch, a socially monogamous pair-bonding species, suggests that the preference for opposite-sex partners may arise in part through the organizing actions of sex steroids. To further investigate this process, zebra finch eggs were injected with 20 microg fadrozole, a potent estrogen synthesis inhibitor, or with the saline vehicle on embryonic day 5. As adults they were given two-choice sexual partner preference tests followed by group aviary tests. Fadrozole females had masculinized beak color and had testes or ovotestes instead of ovaries. Males were not affected by fadrozole; they did not differ from controls on any measure. In contrast, sexual partner preference was substantially masculinized in fadrozole females in the group aviary tests. Untreated males given a choice between fadrozole and untreated females preferred the untreated females, but this was equally the case when they were given a choice between saline-treated and untreated females. These results suggest that males do not specifically avoid females with testes and that male avoidance is unlikely to explain why fadrozole-treated females pair with other females. The present data add to the evidence that actions of gonadal steroids during development contribute to adult sex differences in partner preference in this pair-bonding species. Furthermore, because fadrozole-treated females do not produce audible song, the mechanisms regulating partner preference and song system development are dissociated.