Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA-Bound Platinum Is the Major Determinant of Cisplatin Sensitivity in Head and Neck Squamous Carcinoma Cells

Purpose The combination of systemic cisplatin with local and regional radiotherapy as primary treatment of head and neck squamous cell carcinoma (HNSCC) leads to cure in approximately half of the patients. The addition of cisplatin has significant effects on outcome, but despite extensive research the mechanism underlying cisplatin response is still not well understood. Methods We examined 19 HNSCC cell lines with variable cisplatin sensitivity. We determined the TP53 mutational status of each cell line and investigated the expression levels of 11 potentially relevant genes by quantitative real-time PCR. In addition, we measured cisplatin accumulation and retention, as well as the level of platinum-DNA adducts. Results We found that the IC50 value was significantly correlated with the platinum-DNA adduct levels that accumulated during four hours of cisplatin incubation (p = 0.002). We could not find a significant correlation between cisplatin sensitivity and any of the other parameters tested, including the expression levels of established cisplatin influx and efflux transporters. Furthermore, adduct accumulation did not correlate with mRNA expression of the investigated influx pumps (CTR1 and OCT3) nor with that of the examined DNA repair genes (ATR, ATM, BRCA1, BRCA2 and ERCC1). Conclusion Our findings suggest that the cisplatin-DNA adduct level is the most important determinant of cisplatin sensitivity in HNSCC cells. Imaging with radio-labeled cisplatin might have major associations with outcome.
Nonlinear Dynamics of Infant Sitting Postural Control

Background: Upright sitting is one of the first developmental motor milestones achieved by infants, and sitting postural sway provides a window into the developing motor control system. A variety of posture sway measures can be used, but the optimal measures for infant development have not been identified. Methods: We have collected sitting postural sway data from two groups of infants, one with typical development (n=33), and one with delayed development and either diagnosed with or at risk for cerebral palsy (n=26), when the infants had developed to the point where they could just maintain sitting for about ten seconds. Postural sway data was collected while infants were sitting on a force platform, and the center of pressure was analyzed using both linear and nonlinear measures. Findings: Our results showed that a nonlinear measure, the largest Lyapunov exponent, was the only parameter of postural sway that revealed significant differences between infants with typical versus delayed development. The largest Lyapunov exponent was found to be higher for typically developing infants, indicating less repeated patterning in their movement coordination. Interpretations: A nonlinear measure such as largest Lyapunov exponent may be useful as an identifier of pathology, and thus is a potential candidate for measuring the success of therapeutic interventions.
On the Asymptotic Limit of the Cahn-hilliard Equation

In this paper, we prove, in dimensions 2 and 3, an H 1-version of a conjecture by De Giorgi, namely, the slope of the Allen-Cahn functional with respect to the H −1-structure Gamma-converges to a homogeneous Sobolev norm of the mean curvature of the limiting interface. We will then apply this result to study the asymptotic dynamics of the Cahn-Hilliard equation via the " Gamma convergence " of gradient flows scheme initiated by Sandier and Serfaty. Using a deformation argument, we prove a transport estimate for the Cahn-Hilliard equation by establishing a convergence of the velocity in its natural energy space.
Recreating Daily life in Pompeii

We propose an integrated Mixed Reality methodology for recreating ancient daily life that features realistic simulations of animated virtual human actors (clothes, body, skin, face) who augment real environments and re-enact staged storytelling dramas. We aim to go further from traditional concepts of static cultural artifacts or rigid geometrical and 2D textual augmentations and allow for 3D, interactive, augmented historical character-based event representations in a mobile and wearable setup. This is the main contribution of the described work as well as the proposed extensions to AR Enabling technologies: a VR/AR character simulation kernel framework with real-time, clothed virtual humans that are dynamically superimposed on live camera input, animated and acting based on a predefined, historically correct scenario. We demonstrate such a real-time case study on the actual site of ancient Pompeii.
Assisted Photo Identification of Dermochelys coriacea

Identification marking is a fundamental tool used for conservation, management and research of wild animal populations. For marine turtles, marking is generally accomplished through the use of plastic or metal livestock tags attached to a flipper, or through the use of injected electronic Passive Integrated Transponder (PIT) tags. However, difficulties in applying long-term marking methods on sea turtles have significantly hindered the ability to accurately measure a wide variety of biological and population variables like population size, reproductive output and longevity. One method specifically evaluated on the leatherback sea turtle (Dermochelys coriacea) is the use of photo-identification to identify individual animals. Leatherbacks are listed as critically endangered by the International Union for Conservation of Nature and Natural Resources, see also Eckert et al. [4]. A feature unique to leatherbacks is the presence of the so-called pink spot, a de-pigmented patch located on the dorsal surface of the head, directly over the pineal gland, see Figure 1. Pioneering studies by McDonald and Dutton [6] showed that the shapes of pink spots appeared distinct enough between individuals to be used as a unique identifier. However, as data collections expand, photoidentification by human analysts involves increasingly laborious and tedious browsing through a photo database, up to prohibitive levels. We therefore seek to construct a computer-assisted system, capable of automatically matching pink spot photographs against a database of earlier encounters, with the purpose of identifying individual and remigrant leatherbacks. Because re-sightings are not frequent, one operational requirement is that the risk of overlooking a genuine match should be extremely low. For related work, on other species, see Branzan Albu et al. [1], Ranguelova et al. [7], Van Tienhoven et al. [8] and references therein.
Greedy local-set based sampling and reconstruction for band-limited graph signals

Signal processing on graphs extends signal processing concepts and methodologies from the classical signal processing theory to data indexed by general graphs. Downsampling on graphs is used to efficiently extract valuable information from the massive datasets for reducing the volume of big data. Band-limited graph signal can be reconstructed from sampled data on a sub-set of the vertices by exploiting its spatial correlation. In this paper, we propose a greedy graph signal downsampling method and corresponding reconstruction strategy. We compare the proposed downsampling algorithm with other correlative algorithms on various graph structures for analyzing the reconstruction performance and the robustness, using both synthetic data and real world data. The experimental results demonstrate that the proposed greedy downsampling strategy can achieve satisfactory reconstruction quality and lower sampling rate compared to the correlative algorithms.
Computing optical flow with physical models of brightness variation

This paper exploits physical models of time-varying brightness in image sequences to estimate optical flow and physical parameters of the scene. Previous approaches handled violations of brightness constancy with the use of robust statistics or with generalized brightness constancy constraints that allow generic types of contrast and illumination changes. We consider models of brightness variation that have time-dependent physical causes, namely, changing surface orientation with respect to a directional illuminant, motion of the illuminant, and physical models of heat transport in infrared images. We simultaneously estimate the optical flow and the relevant physical parameters. The estimation problem is formulated using total least squares (TLS), with confidence bounds on the parameters.
Estrogen Regulation of Adiposity and Fuel Partitioning

Menopause is associated with increased adiposity and greater risk of metabolic disease. In the ovariectomized (OVX) rodent model of menopause, increased adiposity is prevented by estrogen (E2) replacement, reflecting both anorexigenic and potentially metabolic actions of E2. To elucidate metabolic and molecular mechanisms by which E2 regulates fat storage and fat mobilization independently of reduced energy intake, C57 BL/6 mice were ovariectomized, randomized to estrogen (OVX-E2) or control pellet implants (OVX-C), and pairfed for 40 days. E2 treatment was associated with reduced adipose mass and adipocyte size and down-regulation of lipogenic genes in adipocytes under the control of sterol-regulatory element-binding protein 1c. Adipocytes of OVX-E2 mice contained >3-fold more perilipin protein than adipocytes of pairfed control (OVX) mice, and this difference was associated with enhanced ex vivo lipolytic response to catecholamines and with greater levels of serum-free fatty acids following fasting. As in adipose tissue, E2 decreased the expression of lipogenic genes in liver and skeletal muscle. In the latter, E2 appears to promote the partitioning of free fatty acids toward oxidation and away from triglyceride storage by up-regulating the expression of peroxisome proliferation activator receptor-δ and its downstream targets and also by directly and rapidly activating AMP-activated protein kinase. Thus, novel genomic and non-genomic actions of E2 promote leanness in OVX mice independently of reduced energy intake.
Critical Information Systems Research: A Habermasian Approach

The paper presents a critical inquiry into the relationship between Computer-Mediated Communication (CMC) and progressive rationalisation in modern organisations. By drawing on the evidence from a field study of a University consultative process, the paper investigates how communicative practices embedded in a public discourse via CMC influence rationalisation of organisational processes. This investigation has been conducted within a theoretical framework of social interaction derived from a particular interpretation of Habermass theory of communicative action in an organisational context. By interpreting electronic messages as linguistic acts and social actions, the paper seeks to provide a new insight into an appropriation and use of CMC. Moreover, by analyzing communicative practices in the light of relationships between social actions, systems rationalisation and lifeworld rationalisation, the paper seeks to explain both visible and hidden impacts of the public discourse via CMC on the organisation.
Rat Hypocretin/Orexin Neurons Are Maintained in a Depolarized State by TRPC Channels

In a previous study we proposed that the depolarized state of the wake-promoting hypocretin/orexin (hcrt/orx) neurons was independent of synaptic inputs as it persisted in tetrodotoxin and low calcium/high magnesium solutions. Here we show first that these cells are hyperpolarized when external sodium is lowered, suggesting that non-selective cation channels (NSCCs) could be involved. As canonical transient receptor channels (TRPCs) are known to form NSCCs, we looked for TRPCs subunits using single-cell RT-PCR and found that TRPC6 mRNA was detectable in a small minority, TRPC1, TRPC3 and TRPC7 in a majority and TRPC4 and 5 in the vast majority (∼90%) of hcrt/orx neurons. Using intracellular applications of TRPC antibodies against subunits known to form NSCCs, we then found that only TRPC5 antibodies elicited an outward current, together with hyperpolarization and inhibition of the cells. These effects were blocked by co-application of a TRPC5 antigen peptide. Voltage-clamp ramps in the presence or absence of TRPC5 antibodies indicated the presence of a current with a reversal potential close to −15 mV. Application of the non-selective TRPC channel blocker, flufenamic acid, had a similar effect, which could be occluded in cells pre-loaded with TRPC5 antibodies. Finally, using the same TRPC5 antibodies we found that most hcrt/orx cells show immunostaining for the TRPC5 subunit. These results suggest that hcrt/orx neurons are endowed with a constitutively active non-selective cation current which depends on TRPC channels containing the TRPC5 subunit and which is responsible for the depolarized and active state of these cells.
High Developmental Rates of Vitrified Bovine Oocytes Following Parthenogenetic Activation, In Vitro Fertilization, and Somatic Cell Nuclear Transfer1

Abstract Successful cryopreservation of mammalian oocytes would provide a steady source of materials for nuclear transfer and in vitro embryo production. Our goal was to develop an effective vitrification protocol to cryopreserve bovine oocytes for research and practice of parthenogenetic activation, in vitro fertilization, and nuclear transfer. Bovine oocytes matured in vitro were placed in 4% ethylene glycol (EG) in TCM 199 plus 20% fetal bovine serum (FBS) at 39°C for 12–15 min, and then transferred to a vitrification solution (35% EG, 5% polyvinyl-pyrrolidone, 0.4 M trehalose in TCM 199 and 20% FBS). Oocytes were vitrified in microdrops on a precooled (−150°C) metal surface (solid-surface vitrification). The vitrified microdrops were stored in liquid nitrogen and were either immediately thawed or were thawed after storage for 2–3 wk. Surviving oocytes were subjected to 1) parthenogenetic activation, 2) in vitro fertilization, or 3) nuclear transfer with cultured adult fibroblast cells. Treated oocytes were cultured in KSOM containing BSA or FBS for 9 to 10 days. Embryo development rates were recorded daily and morphologically high-quality blastocysts were cryopreserved for nuclear transfer-derived embryos at Day 7 or Day 8 of culture. Immediate survival of vitrified/thawed oocytes varied between 77% and 86%. Cleavage and blastocyst development rates of vitrified oocytes following in vitro fertilization or activation were lower than those of the controls. For nuclear transfer, however, vitrified oocytes supported embryonic development as equally well as fresh oocytes.
A systematic review of the survival and complication rates of fixed partial dentures (FPDs) after an observation period of at least 5 years.

OBJECTIVES The objective of this systematic review was to assess the 5- and 10-year survival of implant supported fixed partial dentures (FPDs) and to describe the incidence of biological and technical complications. METHODS An electronic MEDLINE search complemented by manual searching was conducted to identify prospective and retrospective cohort studies on FPDs with a mean follow-up time of at least 5 years. Patients had to have been examined clinically at the follow-up visit. Assessment of the identified studies and data abstraction was performed independently by two reviewers. Failure and complication rates were analyzed using random-effects Poisson regression models to obtain summary estimates of 5- and 10-year survival proportions. RESULTS The search provided 3844 titles and 560 abstracts. Full-text analysis was performed for 176 articles resulting in 21 studies that met the inclusion criteria. Meta-analysis of these studies indicated an estimated survival of implants in implant-supported FPDs of 95.4% (95 percent confidence interval (95% CI): 93.9-96.5%) after 5 and 92.8% (95% CI: 90-94.8%) after 10 years. The survival rate of FPDs supported by implants was 95% (95% CI: 92.2-96.8%) after 5 and 86.7% (95% CI: 82.8-89.8%) after 10 years of function. Only 61.3% (95% CI: 55.3-66.8%) of the patients were free of any complications after 5 years. Peri-implantitis and soft tissue complications occurred in 8.6% (95% CI: 5.1-14.1%) of FPDs after 5 years. Technical complications included implant fractures, connection-related and suprastructure-related complications. The cumulative incidence of implant fractures after 5 years was 0.4% (95% CI: 0.1-1.2%). After 5 years, the cumulative incidence of connection-related complications (screw loosening or fracture) was 7.3% and 14% for suprastructure-related complications (veneer and framework fracture). CONCLUSION Despite a high survival of FPDs, biological and technical complications are frequent. This, in turn, means that substantial amounts of chair time have to be accepted by the clinician following the incorporation of implant-supported FPDs. More studies with follow-up times of 10 and more years are needed as only few studies have described the long-term outcomes.
Thoracic Malignancies and Pulmonary Nodules in Patients under Evaluation for Transcatheter Aortic Valve Implantation (TAVI): Incidence, Follow Up and Possible Impact on Treatment Decision

Background Transcatheter aortic valve implantation (TAVI) has become the treatment of choice in patients with severe aortic valve stenosis who are not eligible for operative replacement and an alternative for those with high surgical risk. Due to high age and smoking history in a high proportion of TAVI patients, suspicious findings are frequently observed in pre-procedural chest computer tomography (CCT). Methods CCT scans of 484 consecutive patients undergoing TAVI were evaluated for incidentally discovered solitary pulmonary nodules (SPN). Results In the entire study population, SPN ≥ 5 mm were found in 87 patients (18%). These patients were compared to 150 patients who were incidentally collected from the 397 patients without SPN or with SPN < 5 mm (control group). After a median follow-up of 455 days, lung cancer was diagnosed in only two patients. Neither SPN ≥ 5 mm (p = 0.579) nor SPN > 8 mm (p = 0.328) were significant predictors of overall survival. Conclusions Despite the high prevalence of SPNs in this single center TAVI cohort lung cancer incidence at midterm follow-up seems to be low. Thus, aggressive diagnostic approaches for incidentally discovered SPN during TAVI evaluation should not delay the treatment of aortic stenosis. Unless advanced thoracic malignancy is obvious, the well documented reduction of morbidity and mortality by TAVI outweighs potentially harmful delays regarding further diagnostics. Standard guideline-approved procedure for SPN can be safely performed after TAVI.
School Libraries and Science Achievement: A View from Michigan's Middle Schools

If strong school library media centers (SLMCs) positively impact middle school student reading achievement, as measured on standardized tests, are they also beneficial for middle school science achievement? To answer this question, the researcher built upon the statistical analyses used in previous school library impact studies with qualitative measures in an attempt to discover relationships between science education and school library media programs. Taking into account major external predictors of student achievement, the researcher examined usage, staffing, collection, technology, and budgetary school library media program variables. She found that 2002 eighth-grade Michigan Educational Assessment Program (MEAP) science test scores had a significant positive relationship only with the size of the SLMC video collection. In subsequent qualitative follow-up activity, participants emphasized the importance of providing video in their services to science educators, as well as their challenges in providing high-quality, current science collections. Participants also pointed to teacher collaboration as a primary but underutilized way of improving their link with science teachers. The results of this study imply that while school library media specialists ably furnish science teachers and students with multimedia resources, due to systemic and professional factors, they are not yet consistently and confidently poised to be science collaborators.
Visual And Active Supervision: Roles, Focus, Technique

Therapists are often thrust into supervisory positions with little preparation. Here is a book that gives them not only the basics of supervision but also creative, active techniques to open up new perspectives on therapeutic situations. Both beginning and experienced supervisors - whether psychologists, social workers, counselors, psychiatrists, or family therapists - will find the discussion and many case illustrations enriching. To help their trainees develop "clinical wisdom" - timing, judgment, and a deep understanding of therapeutic possibility - supervisors play several roles. In turn, they may be teachers, facilitators, consultants, or evaluators. The author defines these roles, as well as their associated functions and precepts, and demonstrates the supervisory stance in each role. Supervisors also focus on one of six areas, three from the therapy system and three from the supervisory system. The adept supervisor will help the trainee-therapist take the experiential learning from one arena and apply it in another. Sometimes trainees are restrained from "hearing" what their supervisor says; the supervisor's advice does not fit with their "map of the world. " Moreover, using words alone, supervisees cannot surprise themselves - they have heard it all before. At those times, in particular, the author recommends visual and active techniques. These methods allow multiple and even contradictory maps or realities to be presented, opening trainees' eyes to new possibilities. Meaning becomes intensely personal, yet systemic. Dramatic and narrative enactments of therapeutic dilemmas, often using evocative objects (for example, magnets of horses, Superman, or the Virgin Mary), capture suchelusive elements as closeness, boundaries, and position, which are the very meat of therapy.
DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach

The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database. Availability The DisoMCS is available at http://cal.tongji. edu.cn/disorder/.