Miracle-dz/UniFAR-FTUs huggingface dataset:
Essential Functions of the Histone Demethylase Lid

Drosophila Little imaginal discs (Lid) is a recently described member of the JmjC domain class of histone demethylases that specifically targets trimethylated histone H3 lysine 4 (H3K4me3). To understand its biological function, we have utilized a series of Lid deletions and point mutations to assess the role that each domain plays in histone demethylation, in animal viability, and in cell growth mediated by the transcription factor dMyc. Strikingly, we find that lid mutants are rescued to adulthood by either wildtype or enzymatically inactive Lid expressed under the control of its endogenous promoter, demonstrating that Lid's demethylase activity is not essential for development. In contrast, ubiquitous expression of UAS-Lid transgenes lacking its JmjN, C-terminal PHD domain, and C5HC2 zinc finger were unable to rescue lid homozygous mutants, indicating that these domains carry out Lid's essential developmental functions. Although Lid-dependent demethylase activity is not essential, dynamic removal of H3K4me3 may still be an important component of development, as we have observed a genetic interaction between lid and another H3K4me3 demethylase, dKDM2. We also show that Lid's essential C-terminal PHD finger binds specifically to di- and trimethylated H3K4 and that this activity is required for Lid to function in dMyc-induced cell growth. Taken together, our findings highlight the importance of Lid function in the regulated removal and recognition of H3K4me3 during development.
Probabilistic Optimization for Energy-Efficient Broadcast in All-Wireless Networks

We study optimization methods for source-initiated energyefficient broadcast in all-wireless networks. The minimum energy broadcast (MEB) problem in wireless networks proved to be NP-complete [1,4]. Past studies on MEB problem [1,2,5,8,9] focus on deterministic optimization to construct energy-efficient broadcast tree. In this paper, we present a probabilistic optimization approach, the Randomized Tree Optimization (RTO) algorithm, which is based on the cross-entropy (CE) method introduced by Rubinstein et al in [3,6,7]. The experimental results indicate that the RTO method obtains the best performance compared to state-of-the-art methods.
Metrics for Community Analysis

Detecting and analyzing dense groups or communities from social and information networks has attracted immense attention over the last decade due to its enormous applicability in different domains. Community detection is an ill-defined problem, as the nature of the communities is not known in advance. The problem has turned even more complicated due to the fact that communities emerge in the network in various forms such as disjoint, overlapping, and hierarchical. Various heuristics have been proposed to address these challenges, depending on the application in hand. All these heuristics have been materialized in the form of new metrics, which in most cases are used as optimization functions for detecting the community structure, or provide an indication of the goodness of detected communities during evaluation. Over the last decade, a large number of such metrics have been proposed. Thus, there arises a need for an organized and detailed survey of the metrics proposed for community detection and evaluation. Here, we present a survey of the start-of-the-art metrics used for the detection and the evaluation of community structure. We also conduct experiments on synthetic and real networks to present a comparative analysis of these metrics in measuring the goodness of the underlying community structure.
Human Umbilical Cord-Derived Mesenchymal Stem Cells Do Not Undergo Malignant Transformation during Long-Term Culturing in Serum-Free Medium

Background Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) are in the foreground as a preferable application for treating diseases. However, the safety of hUC-MSCs after long-term culturing in vitro in serum-free medium remains unclear. Methods hUC-MSCs were separated by adherent tissue culture. hUC-MSCs were cultured in serum-free MesenCult-XF medium and FBS-bases DMEM complete medium. At the 1st, 3rd, 5th, 8th, 10th, and 15th passage, the differentiation of MSCs into osteogenic, chondrogenic, and adipogenic cells was detected, and MTT, surface antigens were measured. Tumorigenicity was analyzed at the 15th passage. Conventional karyotyping was performed at passage 0, 8, and 15. The telomerase activity of hUC-MSCs at passage 1–15 was analyzed. Results Flow cytometry analysis showed that very high expression was detected for CD105, CD73, and CD90 and very low expression for CD45, CD34, CD14, CD79a, and HLA-DR. MSCs could differentiate into osteocytes, chondrocytes, and adipocytes in vitro. There was no obvious chromosome elimination, displacement, or chromosomal imbalance as determined from the guidelines of the International System for Human Cytogenetic Nomenclature. Telomerase activity was down-regulated significantly when the culture time was prolonged. Further, no tumors formed in rats injected with hUC-MSCs (P15) cultured in serum-free and in serum-containing conditions. Conclusion Our data showed that hUC-MSCs met the International Society for Cellular Therapy standards for conditions of long-term in vitro culturing at P15. Since hUC-MSCs can be safely expanded in vitro and are not susceptible to malignant transformation in serum-free medium, these cells are suitable for cell therapy.
Childhood Conditions and Exceptional Longevity

A number of previous studies found interesting links between the early-life experiences and a subsequent mortality in later life. Such findings justify further advancement of these studies by exploring possible links between childhood conditions and exceptional longevity (survival to 100 years). However a number of methodological issues have to be resolved (such as data availability, quality, as well as research approaches), before starting a comprehensive research project on childhood predictors of exceptional longevity. This paper represents an attempt to do a preliminary study of related methodological issues in order to ensure feasibility of the subsequent large-scale research efforts. The following questions are explored in this study: Where to get data on exceptional longevity and childhood conditions? What is the quality of this data, and how can this data quality be checked and improved? What methods of data analysis to use? What are the hypotheses to test, and what are the preliminary findings to validate? The study presents a detailed analysis of available data resources on exceptional longevity and childhood conditions, a rigorous evaluation of data quality and testing different approaches to improve the quality of the data. As a result of these methodological explorations the following multi-step procedure of data collection and data cleaning has being suggested and tested in practice: Step 1. To extract data on alleged centenarians and their childhood conditions from computerized genealogies, pre-selected on the basis of their expected sufficient data quality (a number of indicators of data quality has been identified for this purpose). Following this procedure we extracted detailed family data for 991 alleged centenarians born in 1875-1899 in the United States from publicly available computerized genealogies of 75 million individuals identified in our previous study (Gavrilova, Gavrilov, 1999). Step 2. To validate the claims of exceptional longevity by cross-checking these records with the US Social Security Administration database on deceased person for the entire US population. Step 3. To double-check the validated centenarian claims again for the accuracy of birth date information by matching the records with the early US Censuses (1900, 1910, 1920 and 1930). Step 4. To enhance further the quality of records with confirmed exceptional longevity by adding information on childhood conditions available in the early US Censuses. This multi-step procedure of data collection and quality evaluation is described in this paper in great detail, to demonstrate how this approach works in practice. A new validated dataset on exceptional longevity …
The Cochaperone Bag-1L Enhances Androgen Receptor Action via Interaction with the NH2-Terminal Region of the Receptor

ABSTRACT Members of the Bag-1 family of cochaperones regulate diverse cellular processes including the action of steroid hormone receptors. The largest member of this family, Bag-1L, enhances the transactivation function of the androgen receptor. This occurs primarily through interaction with the NH2 and COOH termini of the receptor. At the NH2 terminus of the receptor, Bag-1L interacts with a region termed τ5. Bag-1M, a naturally occurring variant of Bag-1L that binds to τ5 but is defective in the COOH-terminal interaction, is less efficient in enhancing the transactivation function of the receptor. Surface plasmon resonance and transfection studies showed that the molecular chaperone Hsp70 contributes to the binding of Bag-1L to τ5 and to the regulation of the transactivation function of the androgen receptor. Chromatin immunoprecipitation studies demonstrated that the androgen receptor, Hsp70, and Bag-1L are all targeted to the androgen response elements of the gene that encodes prostate-specific antigen. These studies demonstrate the regulation of transcriptional activity of androgen receptor by a molecular chaperone-cochaperone complex.
Displets: Resolving stereo ambiguities using object knowledge

Stereo techniques have witnessed tremendous progress over the last decades, yet some aspects of the problem still remain challenging today. Striking examples are reflecting and textureless surfaces which cannot easily be recovered using traditional local regularizers. In this paper, we therefore propose to regularize over larger distances using object-category specific disparity proposals (displets) which we sample using inverse graphics techniques based on a sparse disparity estimate and a semantic segmentation of the image. The proposed displets encode the fact that objects of certain categories are not arbitrarily shaped but typically exhibit regular structures. We integrate them as non-local regularizer for the challenging object class `car' into a superpixel based CRF framework and demonstrate its benefits on the KITTI stereo evaluation. At time of submission, our approach ranks first across all KITTI stereo leaderboards.
Topiramate Treatment for Women With Borderline Personality Disorder: A Double-blind, Placebo-Controlled Study

Borderline personality disorder is a common and severe psychiatric illness. The goal of this study was to determine whether topiramate can influence patients' borderline psychopathology, health-related quality of life, and interpersonal problems. Women meeting the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Structured Clinical Interview II criteria for borderline personality disorder were randomly assigned in a 1:1 ratio to topiramate titrated from 25 to 200 mg/d (n = 28) or placebo (n = 28) for 10 weeks. Primary outcome measures were changes on the Symptom-Checklist, on the SF-36 Health Survey, and on the Inventory of Interpersonal Problems. Body weight and additional side effects were assessed weekly. According to the intent-to-treat principle, significant changes (all P < 0.001) on the somatization, interpersonal sensitivity, anxiety, hostility, phobic anxiety, and Global Severity Index scales of the Symptom Checklist were observed in the topiramate-treated subjects after 10 weeks (no significant changes on the obsessive-compulsive, depression, paranoid ideation, and psychoticism scales). In the SF-36 Health Survey, significant differences were observed on all 8 scales (all P < 0.01 or P < 0.001). In the Inventory of Interpersonal Problems, significant differences (all P < 0.001) were found in the scales for overly autocratic, overly competitive, overly introverted, and overly expressive (no significant differences in the scales for overly cold, overly subassertive/subservient, overly exploitable/compliant, and overly nurturant/friendly). Weight loss was additionally observed (p < 0.001). Topiramate appears to be a safe and effective agent in the treatment in women with borderline personality disorder. Additional weight loss can be expected.
The changing role and behaviour of consumers in last mile logistics services: A review

The growth of e-commerce and omnichannel retailing has led to significant changes in urban logistics deliveries. In addition to the traditional delivery channels, new solutions have been introduced, such as click-and-collect, parcel locker delivery, crowdshipping, and on-site delivery. However, such solutions require seamless connections between different layers of the city logistics system. These connections form, in the Physical Internet terminology, a “hyperconnected city”. In this context, how do consumers make decisions about logistics services, either as prospective users or as suppliers of last mile logistics services? We argue that a thorough understanding of consumers’ decision-making about last mile services is a prerequisite for the effective exploration of future demand for these services and the design of transport policies. While there is abundant literature on new approaches of last mile logistics, a review of research on consumers’ decision-making and participation in such services is absent. This paper aims to provide such a review and, based on this, provides directions for future research. Based on the existing literature, we propose a conceptual framework that categorises decisions and system attributes affecting consumers’ decision-making. Highlights for future research include interaction between consumers’ demand and supply decisions, changes in consumer preferences, the importance of social networks, and the city-level impacts of hyperconnected last mile delivery.
Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p

Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine–glycine (so‐called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif. The crystal structure of Xpo1p‐PKI‐Nup42p‐Gsp1p‐GTP complex identified three binding sites for the SxFG/PxFG repeats on HEAT repeats 14–20 of Xpo1p. Mutational analyses of Nup42p showed that the conserved serines and prolines in the SxFG/PxFG repeats contribute to Xpo1p‐Nup42p binding. Our structural and biochemical data suggest that SxFG/PxFG‐Nups such as Nup42p and Nup159p at the cytoplasmic face of NPCs provide high‐affinity docking sites for the Xpo1p nuclear export complex in the terminal stage of NPC passage and that subsequent disassembly of the nuclear export complex facilitates recycling of free Xpo1p back to the nucleus.
Programmed cell cycle arrest is required for infection of corn plants by the fungus Ustilago maydis

Ustilago maydis is a plant pathogen that requires a specific structure called infective filament to penetrate the plant tissue. Although able to grow, this filament is cell cycle arrested on the plant surface. This cell cycle arrest is released once the filament penetrates the plant tissue. The reasons and mechanisms for this cell cycle arrest are unknown. Here, we have tried to address these questions. We reached three conclusions from our studies. First, the observed cell cycle arrest is the result of the cooperation of at least two distinct mechanisms: one involving the activation of the DNA damage response (DDR) cascade; and the other relying on the transcriptional downregulation of Hsl1, a kinase that modulates the G2/M transition. Second, a sustained cell cycle arrest during the infective filament step is necessary for the virulence in U. maydis, as a strain unable to arrest the cell cycle was severely impaired in its ability to infect corn plants. Third, production of the appressorium, a structure required for plant penetration, is incompatible with an active cell cycle. The inability to infect plants by strains defective in cell cycle arrest seems to be caused by their failure to induce the appressorium formation process. In summary, our findings uncover genetic circuits to arrest the cell cycle during the growth of this fungus on the plant surface, thus allowing the penetration into plant tissue.
Solving ill-posed inverse problems using iterative deep neural networks

We propose a partially learned approach for the solution of ill-posed inverse problems with not necessarily linear forward operators. The method builds on ideas from classical regularisation theory and recent advances in deep learning to perform learning while making use of prior information about the inverse problem encoded in the forward operator, noise model and a regularising functional. The method results in a gradient-like iterative scheme, where the ‘gradient’ component is learned using a convolutional network that includes the gradients of the data discrepancy and regulariser as input in each iteration. We present results of such a partially learned gradient scheme on a non-linear tomographic inversion problem with simulated data from both the Sheep-Logan phantom as well as a head CT. The outcome is compared against filtered backprojection and total variation reconstruction and the proposed method provides a 5.4 dB PSNR improvement over the total variation reconstruction while being significantly faster, giving reconstructions of 512×512 pixel images in about 0.4 s using a single graphics processing unit (GPU).
Developing an A Priori Database for Passive Microwave Snow Water Retrievals Over Ocean

A physically optimized a priori database is developed for Global Precipitation Measurement Microwave Imager (GMI) snow water retrievals over ocean. The initial snow water content profiles are derived from CloudSat Cloud Profiling Radar (CPR) measurements. A radiative transfer model in which the single‐scattering properties of nonspherical snowflakes are based on the discrete dipole approximate results is employed to simulate brightness temperatures and their gradients. Snow water content profiles are then optimized through a one‐dimensional variational (1D‐Var) method. The standard deviations of the difference between observed and simulated brightness temperatures are in a similar magnitude to the observation errors defined for observation error covariance matrix after the 1D‐Var optimization, indicating that this variational method is successful. This optimized database is applied in a Bayesian retrieval snow water algorithm. The retrieval results indicated that the 1D‐Var approach has a positive impact on the GMI retrieved snow water content profiles by improving the physical consistency between snow water content profiles and observed brightness temperatures. Global distribution of snow water contents retrieved from the a priori database is compared with CloudSat CPR estimates. Results showed that the two estimates have a similar pattern of global distribution, and the difference of their global means is small. In addition, we investigate the impact of using physical parameters to subset the database on snow water retrievals. It is shown that using total precipitable water to subset the database with 1D‐Var optimization is beneficial for snow water retrievals.
Hot spot temperature for 154 kV transformer filled with mineral oil and natural ester fluid

This paper deals with the hot spot temperature of a transformer when filled with mineral oil, and later on, with natural ester fluid. 14 optical fiber sensors were installed in the 154 kV, 15 MVA transformer filled with mineral oil, with the hot spot temperature measured during the heat run tests. The transformer was retrofilled with natural ester fluid, after which the hot spot temperatures were measured again. For the rated power, the hottest spot temperature was 105.9 °C when the transformer was filled with mineral oil and 129.4 °C when it was filled with natural ester fluid. The hot spot temperature increased by 23.5 °C in the transformer filled with natural ester fluid. This paper applies the hot spot temperature measured using optical fiber sensors to the life curve in natural ester by McShane et al. The life curve of the thermally upgraded kraft paper in natural ester fluid was compared with that in mineral oil, as suggested by the IEEE guide. The life of the transformer filled with natural ester fluid was similar to that filled with mineral oil. Therefore, transformers filled with natural ester fluid do not require increase of cooling pump capacity and surface area of the radiator or reduction of the load to obtain the same life as that of the mineral oil.
Epidemiology of Klebsiella oxytoca-Associated Diarrhea Detected by Simmons Citrate Agar Supplemented with Inositol, Tryptophan, and Bile Salts

ABSTRACT We studied the clinical and epidemiological characteristics of Klebsiella oxytoca-associated diarrhea in hospitalized patients in Hong Kong. Between 1 November 2009 and 30 April 2011, all inositol-fermenting colonies found on Simmons citrate agar supplemented with inositol, tryptophan, and bile salts (SCITB agar) used for the culturing of diarrheal stool samples were screened by a spot indole test for K. oxytoca. The overall sensitivity of SCITB agar plus the spot indole test (93.3%) for the detection of K. oxytoca in stool samples was superior to that of MacConkey agar (63.3%), while the specificities were 100% and 60.4%, respectively. The former achieved a 23-fold reduction in the workload and cost of subsequent standard biochemical identifications. Cytotoxin production and the clonality of K. oxytoca were determined by a cell culture cytotoxicity neutralization assay using HEp-2 cells and pulsed-field gel electrophoresis (PFGE), respectively. Of 5,581 stool samples from 3,537 patients, K. oxytoca was cultured from 117/5,581 (2.1%) stool samples from 104/3,537 (2.9%) patients. Seventy-six of 104 (73.1%) patients with K. oxytoca had no copathogens in their diarrheal stool samples. Twenty-four (31.6%) of 76 patients carried cytotoxin-producing strains, which were significantly associated with antibiotic therapy after hospital admission (50% versus 21.2%; P = 0.01). Health care-associated diarrhea was found in 44 (42%) of 104 patients with K. oxytoca, but there was no epidemiological linkage suggestive of a nosocomial outbreak, and PFGE showed a diverse pattern. None of the patients with cytotoxin-producing K. oxytoca developed antibiotic-associated hemorrhagic colitis, suggesting that K. oxytoca can cause a mild disease manifesting as uncomplicated antibiotic-associated diarrhea with winter seasonality.