Miracle-dz/UniFAR-FTUs huggingface dataset:
Next-generation sequencing-based comprehensive molecular analysis of 43 Japanese patients with cone and cone-rod dystrophies

Purpose To investigate the efficacy of targeted exome sequencing for mutational screening of Japanese patients with cone dystrophy (CD) or cone-rod dystrophy (CRD). Methods DNA samples from 43 Japanese patients with CD or CRD were sequenced using an exome-sequencing panel targeting all 193 known inherited eye disease genes and next-generation sequencing methodologies. Subsequently, candidate variants were screened using systematic data analyses, and their potential pathogenicity was assessed using distinct filtering approaches, which included the frequency of the variants in normal populations, in silico prediction tools, and cosegregation. Results Causative mutations were detected in 12 patients with CD or CRD (27.9%). In total, 14 distinct mutations were identified in the genes ABCA4, CDHR1, CRB1, CRX, GUCY2D, KCNV2, PROM1, PRPH2, and RDH5, including four novel mutations, c.3050+1G>A in ABCA4, c.386A>G in CDHR1, c.652+1_652+4del in CRB1, and c.454G>A in KCNV2. Moreover, a putative pathogenic mutation was identified in RGS9BP, a gene recognized as the source of bradyopsia. Conclusions Targeted exome sequencing effectively identified causative mutations in Japanese patients with CD or CRD. The results confirmed the heterogeneity of the genes responsible for CD and CRD in Japanese populations, as well as the efficacy of targeted exome sequencing-based screening of patients with inherited retinal degeneration.
Integrated waste management in batch chemical industry based on multi-objective optimization

A multi-objective optimization methodology for hazardous liquid waste management is presented in this paper using industrially based LCA models and operating constraints. This approach is used to optimize the handling of waste streams introducing flexible mixing policy scenarios compared to the rigid policy scenarios of the industrial system. It is shown that increasing the degrees of freedom for the waste mixing reduces significantly both the operating cost and the environmental impact by avoiding the use of utilities. Moreover, the influence of waste availability as function of production planning without waste storage is analyzed in several multiperiod optimizations. There, it is demonstrated that this saving potential can be further increased by integration of multiperiod production planning with waste management policies, up to the level of 40% for the environmental impact, and more than 50% for the operating cost, compared to the industrial base case. In some specific cases, a proper matching of production planning and waste mixing policies can also turn the waste treatment into a source of profit exploiting energy production from the incineration process. Implications This study reveals the savings potential of more flexible policies in waste management, in particular waste mixing of liquid waste in batch chemical industries treated in incineration, wet air oxidation, wastewater treatment plants, or recovered by distillation. Through a multi-objective optimization framework including models for operating costs and life-cycle inventories based on industrial data, operating constraints from industrial practice, and terminal constraints from legislation, savings potentials up to 50% for the operation cost and 40% for the environmental impact are demonstrated in two case studies. Supplemental Materials: Supplemental materials are available for this paper. Go to the publisher's online edition of the Journal of the Air & Waste Management Association.
Coded caching with multiple file requests

We study a two-phase caching network consisting of one server with N files connected to K users through an error-free shared link. Each user has a cache memory which can store M files in the placement phase. In the delivery phase, each user requests L files, and the server transmits the messages accordingly. Using the message sent by the server combined with the cache memory, each user reconstructs the L files they requested. In this work, we focus on the case L > 1, i.e., the case of multiple file requests. We adopt the symmetric batch caching scheme and propose a general delivery scheme. To prove the optimality of the proposed general delivery scheme, we apply two converse techniques. The first converse technique is for general coding schemes and is obtained through virtual user construction. The second converse technique is for vector linear coding schemes and is obtained using an interference alignment point of view. With these two converse techniques, we characterize either the unconstrained optimal coding rate, or optimum linear coding rate, with symmetric batch caching for certain cases.
Memory mood congruency phenomenon in bipolar I disorder and major depression disorder patients

The objective of the present study was to evaluate memory performance in tasks with and without affective content (to confirm the mood congruency phenomenon) in acutely admitted patients with bipolar I disorder (BD) and major depression disorder (MDD) and in healthy participants. Seventy-eight participants (24 BD, 29 MDD, and 25 healthy controls) were evaluated. Three word lists were used as the memory task with affective content (positive, negative and indifferent). Psychiatric symptoms were also evaluated with rating scales (Young Mania Rating Scale for mania and Hamilton Depression Rating Scale for depression). Patients were selected during the first week of hospitalization. BD patients showed higher scores in the word span with positive tone than MDD patients and healthy controls (P = 0.002). No other difference was observed for tests with affective tone. MDD patients presented significantly lower scores in the Mini-Mental State Exam, logical memory test, visual recognition span, and digit span, while BD patients presented lower scores in the visual recognition test and digit span. Mood congruency effect was found for word span with positive tone among BD patients but no similar effect was observed among MDD patients for negative items. MDD patients presented more memory impairment than BD patients, but BD patients also showed memory impairment.
On the structure of molecular clouds

We show that the inter-cloud Larson scaling relation between mean volume density and size ρ ∝ R −1 , which in turn implies that mass M ∝ R 2 , or that the column density N is constant, is an artefact of the observational methods used. Specifically, setting the column density threshold near or above the peak of the column density probability distribution function NPDF (N ∼ 10 21 cm −2 ) produces the Larson scaling as long as the N-PDF decreases rapidly at higher column densities. We argue that the physical reasons behind local clouds to have this behaviour are that (1) this peak column density is near the value required to shield CO from photodissociation in the solar neighbourhood, and (2) gas at higher column densities is rare because it is susceptible to gravitational collapse into much smaller structures in specific small regions of the cloud. Similarly, we also use previous results to show that if instead a threshold is set for the volume density, the density will appear to be constant, implying thus that M ∝ R 3 . Thus, the Larson scaling relation does not provide much information on the structure of molecular clouds, and does not imply either that clouds are in Virial equilibrium, or have a universal structure. We also show that the slope of the M–R curve for a single cloud, which transitions from near-to-flat values for large radii to α = 2 as a limiting case for small radii, depends on the properties of the N-PDF.
Characteristics of the Sum of Cross-Components of Triaxial Induction Logging Tool in Layered Anisotropic Formation

There are two nonzero cross-components of a triaxial induction logging tool in the medium coordinate system in a transversely isotropic (TI) formation. The sum of the cross-components holds dependence on only the horizontal conductivities with little nonlinearity and small shoulder bed effect in a horizontally layered formation. Based on the generalized reflection coefficient method, simplified formulas of the sum are derived to analyze its response characteristics. Numerical results show that the apparent conductivity obtained from the sum is a square-looking log with high vertical resolution. Moreover, the readings almost equal to the true horizontal conductivity of the formation beds. These characteristics can be applied to reconstruct the horizontal conductivity and the formation boundaries with triaxial induction logging data.
Suicide in bipolar disorder in a national English sample, 1996–2009: frequency, trends and characteristics

Background Bipolar disorder (BD) has been reported to be associated with high risk of suicide. We aimed to investigate the frequency and characteristics of suicide in people with BD in a national sample. Method Suicide in BD in England from 1996 to 2009 was explored using descriptive statistics on data collected by the National Confidential Inquiry into Suicide and Homicide by People with Mental Illness (NCI). Suicide cases with a primary diagnosis of BD were compared to suicide cases with any other primary diagnosis. Results During the study period 1489 individuals with BD died by suicide, an average of 116 cases/year. Compared to other primary diagnosis suicides, those with BD were more likely to be female, more than 5 years post-diagnosis, current/recent in-patients, to have more than five in-patient admissions, and to have depressive symptoms. In BD suicides the most common co-morbid diagnoses were personality disorder and alcohol dependence. Approximately 40% were not prescribed mood stabilizers at the time of death. More than 60% of BD suicides were in contact with services the week prior to suicide but were assessed as low risk. Conclusions Given the high rate of suicide in BD and the low estimates of risk, it is important that health professionals can accurately identify patients most likely to experience poor outcomes. Factors such as alcohol dependence/misuse, personality disorder, depressive illness and current/recent in-patient admission could characterize a high-risk group. Future studies need to operationalize clinically useful indicators of suicide risk in BD.
Response to rituximab-based therapy and risk factor analysis in Epstein Barr Virus-related lymphoproliferative disorder after hematopoietic stem cell transplant in children and adults: a study from the Infectious Diseases Working Party of the European Group for Blood and Marrow Transplantation.

BACKGROUND The objective of this analysis was to investigate prognostic factors that influence the outcome of Epstein-Barr virus (EBV)-related posttransplant lymphoproliferative disorder (PTLD) after a rituximab-based treatment in the allogeneic hematopoietic stem cell transplant (HSCT) setting. METHODS A total of 4466 allogeneic HSCTs performed between 1999 and 2011 in 19 European Group for Blood and Marrow Transplantation centers were retrospectively analyzed for PTLD, either biopsy-proven or probable disease. RESULTS One hundred forty-four cases of PTLD were identified, indicating an overall EBV-related PTLD frequency of 3.22%, ranging from 1.16% for matched-family donor, 2.86% for mismatched family donor, 3.97% in matched unrelated donors, and 11.24% in mismatched unrelated donor recipients. In total, 69.4% patients survived PTLD. Multivariable analysis showed that a poor response of PTLD to rituximab was associated with an age ≥30 years, involvement of extralymphoid tissue, acute GVHD, and a lack of reduction of immunosuppression upon PTLD diagnosis. In the prognostic model, the PTLD mortality increased with the increasing number of factors: 0-1, 2, or 3 factors being associated with mortality of 7%, 37%, and 72%, respectively (P < .0001). Immunosuppression tapering was associated with a lower PTLD mortality (16% vs 39%), and a decrease of EBV DNAemia in peripheral blood during therapy was predictive of better survival. CONCLUSIONS More than two-thirds of patients with EBV-related PTLD survived after rituximab-based treatment. Reduction of immunosuppression was associated with improved outcome, whereas older age, extranodal disease, and acute graft-vs-host disease predicted poor outcome.
Rewriting the Central European Early Bronze Age Chronology: Evidence from Large-Scale Radiocarbon Dating

The transition from the Neolithic to the Early Bronze Age in Central Europe has often been considered as a supra-regional uniform process, which led to the growing mastery of the new bronze technology. Since the 1920s, archaeologists have divided the Early Bronze Age into two chronological phases (Bronze A1 and A2), which were also seen as stages of technical progress. On the basis of the early radiocarbon dates from the cemetery of Singen, southern Germany, the beginning of the Early Bronze Age in Central Europe was originally dated around 2300/2200 BC and the transition to more complex casting techniques (i.e., Bronze A2) around 2000 BC. On the basis of 140 newly radiocarbon dated human remains from Final Neolithic, Early and Middle Bronze Age cemeteries south of Augsburg (Bavaria) and a re-dating of ten graves from the cemetery of Singen, we propose a significantly different dating range, which forces us to re-think the traditional relative and absolute chronologies as well as the narrative of technical development. We are now able to date the beginning of the Early Bronze Age to around 2150 BC and its end to around 1700 BC. Moreover, there is no transition between Bronze (Bz) A1 and Bronze (Bz) A2, but a complete overlap between the type objects of the two phases from 1900–1700 BC. We thus present a revised chronology of the assumed diagnostic type objects of the Early Bronze Age and recommend a radiocarbon-based view on the development of the material culture. Finally, we propose that the traditional phases Bz A1 and Bz A2 do not represent a chronological sequence, but regionally different social phenomena connected to the willingness of local actors to appropriate the new bronze technology.
Behavioral Indicators of Poor Welfare in Shelter Dogs

We studied behavioral indicators of poor welfare in shelter dogs. Our research question was: How is the welfare of shelter dogs affected by length of stay at a shelter, age, sex, and breed? Data were collected on 18 dogs from October 2016 to March 2017 at a small private shelter in Marietta, GA. Data were collected in 15-minute sessions when the dogs were in their indoor enclosures. No significant differences were found in time spent in abnormal behaviors among dogs that were at the shelter for less than 1 month, 1-6 months, and longer than 6 months, between male and female dogs, between different breeds, and between younger and older dogs. Small sample sizes, individual differences, and an enriched shelter environment could have contributed to the lack of significant findings.
Bohatei: Flexible and Elastic DDoS Defense

DDoS defense today relies on expensive and proprietary hardware appliances deployed at fixed locations. This introduces key limitations with respect to flexibility (e.g., complex routing to get traffic to these "chokepoints") and elasticity in handling changing attack patterns. We observe an opportunity to address these limitations using new networking paradigms such as software-defined networking (SDN) and network functions virtualization (NFV). Based on this observation, we design and implement Bohatei, a flexible and elastic DDoS defense system. In designing Bohatei, we address key challenges with respect to scalability, responsiveness, and adversary-resilience. We have implemented defenses for several DDoS attacks using Bohatei. Our evaluations show that Bohatei is scalable (handling 500 Gbps attacks), responsive (mitigating attacks within one minute), and resilient to dynamic adversaries.
Effect of arbuscular mycorrhizal (AM) fungus and plant growth promoting rhizomicroorganisms (PGPR's) on medicinal plant Solanum viarum seedlings.

A green house nursery study was conducted to assess the interaction between arbuscular mycorrhizal (AM) fungus, Glomus aggregatum and some plant growth promoting rhizomicrooganisms (PGPR's), Bacillus coagulans and Trichoderma harzianum, in soil and their consequent effect on growth, nutrition and content of secondary metabolities of Solanum viarum seedlings. Triple inoculation of G. aggregatum+B. coagulans+T. harzainum with Solanum viarum in a green house nursery study resulted in maximum plant biomass (plant height 105 cm and plant dry weight 12.17 g), P, Fe, Zn, Cu and Mn and secondary metabolities [total phenols (129.6 microg g(-1) f.wt. ), orthodihydroxy phenols (90.6 microg g(-1) f.wt. ), flavonoids (3.94 microg g(-1) f.wt. ), alkaloids (5.05 microg g(-1) f.wt. ), saponins (5.05 microg g(-1) f.wt. ) and tannins (0.324 microg g(-1) f.wt. )] of S. viarum seedlings. The mycorrhizal root colonization and spore numbers in the root zone soil of the inoculated plants increased. The enzyme activity namely acid phosphatase (53.44 microg PNP g(-1) soil), alkaline phosphatase (40.95 microg PNP g(-1) soil) and dehydrogenase (475.5 microg PNP g(-1) soil) and total population of B. coagulans (12.5x10(4) g(-1)) and T. harzianum (12.4 x 10(4) g(-1)), in the root zone soil was found high in the triple inoculation with G. aggregatum+B. coagulans+T. harzianum that proved to be the best microbial consortium.
Structured merge with auto-tuning: balancing precision and performance

Software-merging techniques face the challenge of finding a balance between precision and performance. In practice, developers use unstructured-merge (i.e., line-based) tools, which are fast but imprecise. In academia, many approaches incorporate information on the structure of the artifacts being merged. While this increases precision in conflict detection and resolution, it can induce severe performance penalties. Striving for a proper balance between precision and performance, we propose a structured-merge approach with auto-tuning. In a nutshell, we tune the merge process on-line by switching between unstructured and structured merge, depending on the presence of conflicts. We implemented a corresponding merge tool for Java, called JDime. Our experiments with 8 real-world Java projects, involving 72 merge scenarios with over 17 million lines of code, demonstrate that our approach indeed hits a sweet spot: While largely maintaining a precision that is superior to the one of unstructured merge, structured merge with auto-tuning is up to 12 times faster than purely structured merge, 5 times on average.
Optimal design of two-qubit quantum circuits

Current quantum computing hardware is unable to sustain quantum coherent operations for more than a handful of gate operations. Consequently, if near-term experimental milestones, such as synthesizing arbitrary entangled states, or performing fault-tolerant operations, are to be met, it will be necessary to minimize the number of elementary quantum gates used. In order to demonstrate non-trivial quantum computations experimentally, such as the synthesis of arbitrary entangled states, it will be useful to understand how to decompose a desired quantum computation into the shortest possible sequence of one-qubit and two-qubit gates. We contribute to this effort by providing a method to construct an oprimal quantum circuit for a general two-qubit gate that requires at most 3 CNOT gates and 15 elementary onequbit gates. Moreover, if the desired two-qubit gate corresponds to a purely real unitary transformation, we provide a construction that requires at most 2 CNOTs and 12 onequbit gates. We then prove that these constructions are optimal with respect to the family of CNOT, y-rotation, z-rotation, and phase gates.
Least squares conformal maps for automatic texture atlas generation

A Texture Atlas is an efficient color representation for 3D Paint Systems. The model to be textured is decomposed into charts homeomorphic to discs, each chart is parameterized, and the unfolded charts are packed in texture space. Existing texture atlas methods for triangulated surfaces suffer from several limitations, requiring them to generate a large number of small charts with simple borders. The discontinuities between the charts cause artifacts, and make it difficult to paint large areas with regular patterns.In this paper, our main contribution is a new quasi-conformal parameterization method, based on a least-squares approximation of the Cauchy-Riemann equations. The so-defined objective function minimizes angle deformations, and we prove the following properties: the minimum is unique, independent of a similarity in texture space, independent of the resolution of the mesh and cannot generate triangle flips. The function is numerically well behaved and can therefore be very efficiently minimized. Our approach is robust, and can parameterize large charts with complex borders.We also introduce segmentation methods to decompose the model into charts with natural shapes, and a new packing algorithm to gather them in texture space. We demonstrate our approach applied to paint both scanned and modeled data sets.
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
Shape memory alloys : modeling and engineering applications

to Shape Memory Alloys. - Thermomechanical Characterization of Shape Memory Alloy Materials. - Thermomechanical Constitutive Modeling of SMAs. - Numerical Implementation of an SMA Thermomechanical Constitutive Model Using return Mapping Algorithms. - Modeling of Transformation-Induced Plasticity in SMAs. - Extended SMA Modeling. - Modeling of Magnetic SMAs.