Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Porcine Intervertebral Disc Matrix on Stem Cell Differentiation

For back disorders, cell therapy is one approach for a real regeneration of a degenerated nucleus pulposus. Human mesenchymal stem cells (hMSC) could be differentiated into nucleus pulposus (NP)-like cells and used for cell therapy. Therefore it is necessary to find a suitable biocompatible matrix, which supports differentiation. It could be shown that a differentiation of hMSC in a microbial transglutaminase cross-linked gelatin matrix is possible, but resulted in a more chondrocyte-like cell type. The addition of porcine NP extract to the gelatin matrix caused a differentiation closer to the desired NP cell phenotype. This concludes that a hydrogel containing NP extract without any other supplements could be suitable for differentiation of hMSCs into NP cells. The NP extract itself can be cross-linked by transglutaminase to build a hydrogel free of NP atypical substrates. As shown by side-specific biotinylation, the NP extract contains molecules with free glutamine and lysine residues available for the transglutaminase.
Manufacturing of periodical nanostructures by fs-laser direct writing

Sub wavelength ripples (spacing < λ/4) perpendicular to the polarisation of the laser radiation are obtained by scanning a tightly focused beam (~1μm) of femtosecond laser radiation from a Ti:Sapphire laser (τ =100fs, λ =800nm & 400nm, f=1kHz) and from a Yb:glass fiber laser (τ =400fs, λ =1045nm, f=0.1-5MHz) over the surface of various materials like amorphous Nd:Gd3Ga5O12 films 1 μm in thickness on YAG substrates, diamond, polytetrafluoroethylene, LiF, MgF2, ZBLAN, Al2O3, LiNbO3, SiO2, Si, Cu and Au. The ripple patterns extend coherently over many overlapping laser pulses and scanning tracks. Investigated are the dependence of the ripple spacing Λ on the material, the lateral distance of the laser pulses, the N.A. of the focussing optics, the repetition rate and the applied wavelength. The ripples are characterised using electron microscopy. Some possible models for the origin of the ripple growth are discussed and conditions under which these phenomena occur are contained. New results concerning the scaling of the production process using a high repetition rate laser and a fast translation stage are demonstrated. Potential applications are presented and consequences for precise nano- and microstructuring using ultra short pulsed lasers are discussed.
Practice of Epidemiology Identification of Patients With Nonmelanoma Skin Cancer Using Health Maintenance Organization Claims Data

Cancer registries usually exclude nonmelanoma skin cancers (NMSC), despite the large population affected. Health maintenance organization (HMO) and health system administrative databases could be used as sampling frames for ascertaining NMSC. NMSC patients diagnosed between January 1, 1988, and December 31, 2007, from such defined US populations were identified by using 3 algorithms: NMSC International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes, NMSC treatment Current Procedural Terminology (CPT) codes, or both codes. A subset of charts was reviewed to verify NMSC diagnosis, including all records from HMO-enrollee members in 2007. Positive predictive values for NMSC ascertainment were calculated. Analyses of data from 1988–2007 ascertained 11,742 NMSC patients. A random sample of 965 cases was selected for chart review, and NMSCs were validated in 47.0% of ICD-9-CM–identified patients, 73.4% of CPT-identified patients, and 94.9% identified with both codes. All charts from HMO–health plan enrollees in 2007 were reviewed (n 1⁄4 1,116). Cases of NMSC were confirmed in 96.5% of ICD-9-CM–identified patients, 98.3% of CPT-identified patients, and 98.7% identified with both codes. HMO administrative data can be used to ascertain NMSC with high positive predictive values with either ICD-9-CM or CPT code, but both codes may be necessary among non-HMO patient populations.
Phase retrieval and norm retrieval

Phase retrieval has become a very active area of research. We will classify when phase retrieval by Parseval frames passes to the Naimark complement and when phase retrieval by projections passes to the orthogonal complements. We introduce a new concept we call norm retrieval and show that this is what is necessary for passing phase retrieval to complements. This leads to a detailed study of norm retrieval and its relationship to phase retrieval. One fundamental result: a frame $\{\varphi_i\}_{i=1}^M$ yields phase retrieval if and only if $\{T\varphi_i\}_{i=1}^M$ yields norm retrieval for every invertible operator $T$.
All-trans Retinoic Acid Inhibits Type 1 Diabetes by T Regulatory (Treg)-Dependent Suppression of Interferon-γ–Producing T-cells Without Affecting Th17 Cells

OBJECTIVE—All-trans retinoic acid (ATRA), a potent derivative of vitamin A, can regulate immune responses. However, its role in inducing immune tolerance associated with the prevention of islet inflammation and inhibition of type 1 diabetes remains unclear. RESEARCH DESIGN AND METHODS—We investigated the mechanisms underlying the potential immunoregulatory effect of ATRA on type 1 diabetes using an adoptive transfer animal model of the disease. RESULTS—Our data demonstrated that ATRA treatment inhibited diabetes in NOD mice with established insulitis. In addition, it suppressed interferon (IFN)-γ–producing CD4+ and CD8+ T effector (Teff) cells and expanded T regulatory (Treg) cells in recipient mice transferred with diabetic NOD splenocytes, without affecting either interleukin (IL)-17 –or IL-4–producing cells. Consistent with these results, ATRA reduced T-bet and STAT4 expression in T-cells and decreased islet-infiltrating CD8+ T-cells, suppressing their activation and IFN-γ/granzyme B expression. Depletion of CD4+CD25+ Treg cells impaired the inhibitory effect of ATRA on islet-infiltrating T-cells and blocked its protective effect on diabetes. Therefore, ATRA treatment induced Treg cell–dependent immune tolerance by suppressing both CD4+ and CD8+ Teff cells while promoting Treg cell expansion. CONCLUSIONS—These results demonstrate that ATRA treatment promoted in vivo expansion of Treg cells and induced Treg cell–dependent immune tolerance by suppressing IFN-γ–producing T-cells, without affecting Th17 cells. Our study also provides novel insights into how ATRA induces immune tolerance in vivo via its effects on Teff and Treg cells.
Effect of two stunning methods on postmortem muscle pH and meat quality of common carp (Cyprinus carpio L.).

Percussive and electrical stunning are the most promising methods in terms of rendering fish unconscious prior to slaughter. The aim of this study was to determine the effect of these two stunning methods on postmortem muscle changes and meat quality of common carps. The experimental fish were stunned either by percussion (Group 1) or by electrical current application (Group 2), both followed by immediate decapitation. Muscle pH was measured at different time intervals to assess the postmortem metabolic changes, whereas meat colour, drip loss and water activity were used as quality parameters. The fish in Group 1 showed slightly accelerated postmortem muscle metabolism, higher redness (a*) and yellowness (b*) colour values and lower water activity. Percentage of drip loss after 4 days of storage at 4 °C did not differ significantly between the two groups. Based on the obtained results we concluded that both tested stunning methods were not associated with high levels of stress and significant detrimental effect on the meat quality of common carps.
Characterization of RAD9 of Saccharomyces cerevisiae and evidence that its function acts posttranslationally in cell cycle arrest after DNA damage

In eucaryotic cells, incompletely replicated or damaged chromosomes induce cell cycle arrest in G2 before mitosis, and in the yeast Saccharomyces cerevisiae the RAD9 gene is essential for the cell cycle arrest (T.A. Weinert and L. H. Hartwell, Science 241:317-322, 1988). In this report, we extend the analysis of RAD9-dependent cell cycle control. We found that both induction of RAD9-dependent arrest in G2 and recovery from arrest could occur in the presence of the protein synthesis inhibitor cycloheximide, showing that the mechanism of RAD9-dependent control involves a posttranslational mechanism(s). We have isolated and determined the DNA sequence of the RAD9 gene, confirming the DNA sequence reported previously (R. H. Schiestl, P. Reynolds, S. Prakash, and L. Prakash, Mol. Cell. Biol. 9:1882-1886, 1989). The predicted protein sequence for the Rad9 protein bears no similarity to sequences of known proteins. We also found that synthesis of the RAD9 transcript in the cell cycle was constitutive and not induced by X-irradiation. We constructed yeast cells containing a complete deletion of the RAD9 gene; the rad9 null mutants were viable, sensitive to X- and UV irradiation, and defective for cell cycle arrest after DNA damage. Although Rad+ and rad9 delta cells had similar growth rates and cell cycle kinetics in unirradiated cells, the spontaneous rate of chromosome loss (in unirradiated cells) was elevated 7- to 21-fold in rad9 delta cells. These studies show that in the presence of induced or endogenous DNA damage, RAD9 is a negative regulator that inhibits progression from G2 in order to preserve cell viability and to maintain the fidelity of chromosome transmission.
Cement based overlay for orthotropic steel bridge decks: A Multi-Scale Modeling Approach

The success of the traditional orthotropic steel bridge deck may be due to its high strength to weight ratio. However, fatigue damage has been experienced within heavily trafficked routes due to the low stiffness of this deck in combination with increasing traffic intensity and wheel pressure. This thesis investigates a system to stiffen an orthotropic steel bridge deck, using a cement-based overlay. The investigation is based on nonlinear fracture mechanics and aims to determine the performance of the bridge deck in terms of cracking behavior. The main goal of applying a cement-based overlay to an orthotropic steel bridge deck, is to increase the deck stiffness and thereby reduce the stresses in fatigue sensitive steel parts. Cracking of the cement-based overlay will have considerable influence on the composite action and durability of the system. The system has to be economically beneficial and show a good performance with regards to cracking behavior. Since cracking plays a major role on the performance, cracking behavior of the overlay is the main focus of the present thesis. The strategy utilized in the present thesis is based on multi scale modeling, which spans from modeling and experiments on the steel-concrete interface scale, to modeling of a real size structure. The multi scale concept is utilized by identifying mechanical behavior on the steel-concrete interface scale and later applying the mechanical behavior on the structural scale. On the steel-concrete interface scale, normal cracking (Mode I) and combined normal and shear cracking (mixed mode cracking) are analyzed through experiments and modeling. The aim and outcome of the study on the interface scale, is a set of constitutive parameters which later are applied on the structural scale. The composite action between an overlay and steel plate is analyzed experimentally through small beam and plate elements with spans in the range of 0.8 to 1.0 meter. Through these tests, the numerical tools applied are verified by comparing experimental results to numerical results. Cracking between the overlay and steel plate (debonding) is also analyzed through small scale experiments and further investigated numerically. The investigation shows that debonding is initiated from a defect in the overlay, e.g. an overlay crack. Debonding initiation is observed for a certain crack width of the overlay. Significant findings on the composite elements, such as the overlay crack width which initiates debonding, are also observed when modeling a full size structure. A set of theoretical tools have been established to analyze the performance of an orthotropic steel bridge deck stiffened with a cement-based overlay, with respect to cracking behavior. For a given design situation, it might be possible to give an estimate on the crack pattern and maximum crack width when applying a given cement-based overlay.
O ct 2 00 7 Branes on Poisson varieties

We first extend the notion of connection in the context of Courant algebroids to obtain a new characterization of generalized Kähler geometry. We then establish a new notion of isomorphism between holomorphic Poisson manifolds, which is non-holomorphic in nature. Finally we show an equivalence between certain configurations of branes on Poisson varieties and generalized Kähler structures, and use this to construct explicitly new families of generalized Kähler structures on compact holomorphic Poisson manifolds equipped with positive Poisson line bundles (e.g. Fano manifolds). We end with some speculations concerning the connection to non-commutative algebraic geometry.
Supercritical Extraction from Vinification Residues: Fatty Acids, α-Tocopherol, and Phenolic Compounds in the Oil Seeds from Different Varieties of Grape

Supercritical fluid extraction has been widely employed in the extraction of high purity substances. In this study, we used the technology to obtain oil from seeds from a variety of grapes, from vinification residues generated in the Southern region of the state of Rio Grande do Sul, Brazil. This work encompasses three varieties of Vitis vinifera (Moscato Giallo, Merlot, and Cabernet Sauvignon) and two of Vitis labrusca (Bordô e Isabel), harvested in 2005 and 2006. We obtained the highest oil content from Bordô (15.40%) in 2005 and from Merlot (14.66%), 2006. The biggest concentration of palmitic, stearic, and linoleic acids was observed in Bordô, 2005, and in Bordô, Merlot, and Moscato Giallo, 2006. Bordô showed the highest concentration of oleic acid and α-tocopherol in both seasons too. For the equivalent of procyanidins, we did not notice significant difference among the varieties from the 2005 harvest. In 2006, both varieties Isabel and Cabernet Sauvignon showed a value slightly lower than the other varieties. The concentration of total phenolics was higher in Bordô and Cabernet Sauvignon. The presence of these substances is related to several important pharmacological properties and might be an alternative to conventional processes to obtain these bioactives.
Mutant identifying a third recombination group in a bunyavirus

Only two recombination groups have been reported in genetic analyses of ts mutants of 10 different bunyaviruses from the Bunyamwera and California encephalitis serogroups, although three groups are expected from the tripartite structure of the genome of all members of the family Bunyaviridae. We describe now a ts mutant of Maguari virus, MAGts23(III), which recombined in both vertebrate (BHK-21) and invertebrate (Aedes albopictus) cells with mutants representing recombination groups I and II of this Bunyamwera serogroup virus. In addition, MAGts23(III) recombined with two mutants MAGts20 and MAGts21, provisionally identified as double mutants by their failure to recombine with group I or group II mutants, Mutant MAGts23(III) therefore represents a third bunyavirus recombination group. Mutant MAGts23(III) differed phenotypically from other bunyavirus mutants by growth restriction in BS-C-1 cells. Wild-type recombinants were obtained in the heterologous cross of MAGts23(III) and a group II mutant of Bunyamwera virus, but not in a cross with a group I mutant. The recombinants had the G protein of the Maguari virus parent and the N protein of the Bunyamwera virus parent. Analysis of the phenotypes of clones isolated at permissive temperature from the progeny of the other cross [MAGts23(III) and a group I mutant of Bunyamwera virus] indicated that recombination occurred in this cross, but that the possible recombinant phenotypes were not recovered with equal frequency. As a consequence, it has not been possible to obtain a gene assignment for group III from genetic data alone.
Sequence Divergent RXLR Effectors Share a Structural Fold Conserved across Plant Pathogenic Oomycete Species

The availability of genome sequences for some of the most devastating eukaryotic plant pathogens has led a revolution in our understanding of how these parasites cause disease, and how their hosts respond to invasion [1]–[7]. One of the most significant discoveries from the genome sequences of plant pathogenic oomycetes is the plethora of putative translocated effector proteins these organisms encode. Many effector genes display signatures of rapid evolution and tend to reside in dynamic regions of the pathogen genomes. Once inside the host, effector proteins modulate cellular processes, mainly suppressing plant immunity [8]–[12]. Effectors can also be recognized directly or indirectly by the plant immune system through the action of disease resistance (R) proteins [13], [14].
The Columbia Cooperative Aging Program: An Interdisciplinary and Interdepartmental Approach to Geriatric Education for Medical Interns

Although there is a critical need to prepare physicians to care for the growing population of older adults, many academic medical centers lack the geriatric‐trained faculty and dedicated resources needed to support comprehensive residency training programs in geriatrics. Because of this challenge at Columbia University, the Columbia Cooperative Aging Program was developed to foster geriatric training for medical interns. For approximately 60 interns each year completing their month‐long geriatric rotations, an integral part of this training now involves conducting comprehensive assessments with “well” older people, supervised by an interdisciplinary team of preceptors from various disciplines, including cardiology, internal medicine, occupational therapy, geriatric nursing, psychiatry, education, public health, social work, and medical anthropology.
Practical Context-Sensitive CFI

Current Control-Flow Integrity (CFI) implementations track control edges individually, insensitive to the context of preceding edges. Recent work demonstrates that this leaves sufficient leeway for powerful ROP attacks. Context-sensitive CFI, which can provide enhanced security, is widely considered impractical for real-world adoption. Our work shows that Context-sensitive CFI (CCFI) for both the backward and forward edge can be implemented efficiently on commodity hardware. We present PathArmor, a binary-level CCFI implementation which tracks paths to sensitive program states, and defines the set of valid control edges within the state context to yield higher precision than existing CFI implementations. Even with simple context-sensitive policies, PathArmor yields significantly stronger CFI invariants than context-insensitive CFI, with similar performance.
Detecting Coordination Problems in Collaborative Software Development Environments

Abstract Software development is rarely an individual effort and generally involves teams of developers collaborating to generate good reliable code. Among the software code there exist technical dependencies that arise from software components using services from other components. The different ways of assigning the design, development, and testing of these software modules to people can cause various coordination problems among them. We claim that the collaboration of the developers, designers and testers must be related to and governed by the technical task structure. These collaboration practices are handled in what we call Socio-Technical Patterns. The TESNA project (Technical Social Network Analysis) we report on in this paper addresses this issue. We propose a method and a tool that a project manager can use in order to detect the socio-technical coordination problems. We test the method and tool in a case study of a small and innovative software product company.
Reduced phosphoCREB in Müller glia during retinal degeneration in rd10 mice

Purpose The mechanisms that trigger retinal degeneration are not well understood, despite the availability of several animal models with different mutations. In the present report, the rd10 mouse, a model for retinitis pigmentosa (RP) that contains a mutation in the gene for PDE6β (Pde6b), is used to evaluate gliosis, as a marker for retinal stress, and cyclic AMP response element binding protein (CREB) phosphorylation, which may be important early in retinal degeneration. Methods Wild-type C57Bl6J and rd10 mice raised under cyclic light were examined for changes in gliosis and CREB phosphorylation for approximately 3 weeks beginning at P14 to P17 using immunocytochemistry. Mice raised under normal cyclic light and in complete darkness were also compared for changes in CREB phosphorylation. Results Gliosis in rd10 mice raised under cyclic light was apparent at P17, before extensive degeneration of the photoreceptor layer is visible, and increased over time. Phosphorylation of CREB at Ser133 (pCREB) was detected in Müller glia (MG) in the wild-type and rd10 mice. However, at all phases of photoreceptor degeneration, the pCREB levels were lower in the rd10 mice. We also observed extensive migration of MG cell bodies to the outer nuclear layer (ONL) during degeneration. In contrast to the mice raised under cyclic light, the rd10 mice raised in the dark exhibited slower rates of degeneration. When the dark-reared mice were exposed to cyclic light, the photoreceptor layer degenerated within 4 days to approximately one to two rows of nuclei. Interestingly, the pCREB levels in the MG also decreased during this 4-day cyclic light exposure compared to the levels in the rd10 mice raised continuously in the dark. Conclusions The results of these studies suggest that photoreceptors communicate directly or indirectly with MG at early stages, inducing gliosis before extensive retinal degeneration is apparent in rd10 mice. Surprisingly, phosphorylation of CREB is downregulated in the MG. These results raise the interesting possibility that Müller glia undergo CREB-mediated transcriptional changes that influence photoreceptor degeneration either positively or negatively. Unlike canine models of RP, no increase in pCREB was observed in photoreceptor cells during this period suggesting possible mechanistic differences in the role of CREB in photoreceptors between these species.