Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical Inhibitors of Non-Homologous End Joining Increase Targeted Construct Integration in Cryptococcus neoformans

The development of a biolistic transformation protocol for Cryptococcus neoformans over 25 years ago ushered in a new era of molecular characterization of virulence in this previously intractable fungal pathogen. However, due to the low rate of homologous recombination in this species, the process of creating targeted gene deletions using biolistic transformation remains inefficient. To overcome the corresponding difficulty achieving molecular genetic modifications, members of the Cryptococcus community have investigated the use of specific genetic backgrounds or construct design strategies aimed at reducing ectopic construct integration via non-homologous end joining (NHEJ). One such approach involves deletion of components of the NHEJ-associated Ku heterodimer. While this strategy increases homologous recombination to nearly 100%, it also restricts strain generation to a ku80Δ genetic background and requires subsequent complex mating procedures to reestablish wild-type DNA repair. In this study, we have investigated the ability of known inhibitors of mammalian NHEJ to transiently phenocopy the C. neoformans Ku deletion strains. Testing of eight candidate inhibitors revealed a range of efficacies in C. neoformans, with the most promising compound (W7) routinely increasing the rate of gene deletion to over 50%. We have successfully employed multiple inhibitors to reproducibly enhance the deletion rate at multiple loci, demonstrating a new, easily applied methodology to expedite acquisition of precise genetic alterations in C. neoformans. Based on this success, we anticipate that the use of these inhibitors will not only become widespread in the Cryptococcus community, but may also find use in other fungal species as well.
Persian speech emotion recognition

Speech emotion recognition is one of the most challenging and the most interesting topics of the voice processing research in recent years. Performance enhancement and computational complexity mitigation are the subject matter of the current study. Current study proposes a speech emotion recognition method by employing HMM-based classifier and minimum number of features in the Persian language. Result illustrate the proposed method is able to recognizing eight emotional states of anger, happy, sadness, neutral, surprise, disgust, fear and boredom up to 79.50% average accuracy. In contrast to previous researches, the proposed method provides 8.72% improvement.
Stability of the Endosomal Scaffold Protein LAMTOR3 Depends on Heterodimer Assembly and Proteasomal Degradation*

Background: LAMTOR3 is an endosomal MAPK scaffold recently shown also to modulate the mTORC1 pathway. Results: Association to LAMTOR2 and recruitment to the endosomal membrane stabilize LAMTOR3 and prevent the premature degradation of the protein by the proteasome. Conclusion: The ubiquitin-proteasome pathway and LAMTOR complex assembly tightly control LAMTOR3 abundance. Significance: Cells may modulate the dual ERK/mTORC1 activity of LAMTOR3 by tightly controlling its intracellular protein level. LAMTOR3 (MP1) and LAMTOR2 (p14) form a heterodimer as part of the larger Ragulator complex that is required for MAPK and mTOR1 signaling from late endosomes/lysosomes. Here, we show that loss of LAMTOR2 (p14) results in an unstable cytosolic monomeric pool of LAMTOR3 (MP1). Monomeric cytoplasmic LAMTOR3 is rapidly degraded in a proteasome-dependent but lysosome-independent manner. Mutational analyses indicated that the turnover of the protein is dependent on ubiquitination of several lysine residues. Similarly, other Ragulator subunits, LAMTOR1 (p18), LAMTOR4 (c7orf59), and LAMTOR5 (HBXIP), are degraded as well upon the loss of LAMTOR2. Thus the assembly of the Ragulator complex is monitored by cellular quality control systems, most likely to prevent aberrant signaling at the convergence of mTOR and MAPK caused by a defective Ragulator complex.
Toward the Graphics Turing Scale on a Blue Gene Supercomputer

We investigate raytracing performance that can be achieved on a class of Blue Gene supercomputers. We measure a 822 times speedup over a Pentium IV on a 6144 processor Blue Gene/L. We measure the computational performance as a function of number of processors and problem size to determine the scaling performance of the raytracing calculation on the Blue Gene. We find nontrivial scaling behavior at large number of processors. We discuss applications of this technology to scientific visualization with advanced lighting and high resolution. We utilize three racks of a Blue Gene/L in our calculations which is less than three percent of the the capacity of the worlds largest Blue Gene computer.
Performance of LTE communication system in correlated rayleigh channel with different antenna configurations

Long Term Evolution (LTE) standard supports MU-MIMO as a new technology to take advantage of the inherent properties of MIMO technology in improving the spectral efficiency and to support multiple users simultaneously. This paper studies the performance of the SC-OFDMA-based LTE system in the uplink correlated Rayleigh fading channel in terms of bit error rate (BER). To the best of author knowledge, the performance of such an LTE system incorporating Successive Interference Cancellation Minimum Mean Square Error (SICMMSE) receiver in correlated Rayleigh channel was not previously investigated, more particularly with different antenna configurations. The choice of such a receiver is motivated by its relative complexity and computation reduction.
Bullying behaviour, empathy and social cognition: Cool manipulators or social misfits?

While aggressive behaviour is often characterised by deficits in social information processing, bullying, a subcategory of aggression, is generally engaged in by those who have been found to have a good understanding of how others are thinking and feeling. What is not known is if this understanding is used in the same way by different types of bullies. The current study investigated if relational bullies, those who include social relationship manipulation in their bullying, have higher cognitive empathy and social cognition skills, but lower emotional empathy than other types of bullies and non-bullies. A sample of 187 Australian secondary and tertiary undergraduate students participated in this study. All completed the Little, Johns, Henrich and Hawley (2003) Aggression Questionnaire, the Interpersonal Reactivity Index, and responded to two vignettes. Contrary to previous research no significant difference was found between any of the bullying and non-bullying groups on empathy and social cognition. However, the relationship between aggression and empathy was found to be different for males and females, which may have implications for bullying intervention programs.
Parallel input/output with heterogeneous disks

Panda is a high performance library for accessing large multidimensional array data on secondary storage of parallel platforms and networks of workstations. When using Panda as the I/O component of a scientific application, H3expresso, on the IBM SP2 at Cornell Theory Center, we found that some nodes are more powerful with respect to I/O than others, requiring the introduction of load balancing techniques to maintain high performance. We expect that heterogeneity will also be a big issue for DBMSs or parallel I/O libraries designed for scientific applications running on networks of workstations, and the methods of allocating data to servers in these environments will need to be upgraded to take heterogeneity into account, while still allowing users to exert control over data layout. We propose such an approach to load balancing, under which we respect the user's choice of high level disk layout, but introduce automatic subchunking. The use of subchunks allows us to divide the very large chunks typically specified by the user's disk layout into more manageable size units that can be allocated to I/O nodes in a manner that fairly distributes the load. We also present two techniques for allocating subchunks to nodes, static and dynamic, and evaluate their performance on the SP2.
Using Goal Modeling and OntoUML for Reengineering the Good Relations Ontology

Ontologies have been used as vehicles to assign semantics to data in several domains, since they represent a conceptualization about the domain of interest and establish a common vocabulary to be shared. For properly addressing the domain of interest and serving as a means to attribute meaning to data, ontology should provide a correct understanding of the domain conceptualization. This paper presents some results of an ontological analysis of the Good Relations Ontology (GRO). For the ontological analysis, we used Goal Modeling to delimitate the ontology scope and the Unified Foundational Ontology to analyze its conceptual model. Our analysis discovered several limitations that prevent GRO from properly addressing the domain of interest. Thus, we reengineered GRO to correct such limitations, and implemented it using OWL.
MUC1 Expression in Intramucosal Colorectal Neoplasms

Purpose: The mucin core peptide MUC1 often is detectable in colorectal carcinoma (CRC) tissue and cell lines. However, whether MUC1 in CRC correlates with tumor histogenesis and progression is unclear. We studied the relationship between MUC1 expression in intramucosal CRC and clinicopathologic features, expression of Ki-67, and p53 protein, and apoptosis. Methods: The intramucosal CRC we studied included 140 endoscopically or surgically resected lesions, including 106 low-grade carcinomas and 34 high-grade carcinomas. De novo carcinoma, defined as carcinoma with no adenomatous component, represented 9 of 140 tumors. Three macroscopic types were identified: 57 lesions were polypoid, 55 were superficial and flat, and 28 were granular-type laterally spreading tumors (G-LST). MUC1, Ki-67, and p53 expression were examined immunohistochemically. Apoptotic cells were identified by in situ DNA nick end labeling. Results: MUC1 expression in high-grade carcinomas was significantly more frequent (p < 0.01) than in low-grade carcinomas; expression in adenomas was almost nil. MUC1 expression in polypoid carcinomas was significantly more frequent (p < 0.05) than in superficial carcinomas or G-LST. MUC1 expression in carcinomas with p53 expression was significantly more frequent (p < 0.01) than in carcinomas not expressing p53. No significant correlation was found between expression of MUC1 and Ki-67 labeling index. MUC1 was expressed more frequently in carcinomas with relatively high apoptotic index (p < 0.01). MUC1 expression did not differ between de novo carcinomas and those developing from adenomas. Conclusions: The results suggest that MUC1 is likely to be expressed in the course of colorectal carcinoma development when p53 protein is overexpressed and apoptosis is prominent.
A Method of Setting the Order of User Story Development of an Agile-Waterfall Hybrid Method by Focusing on Common Objects

In developing enterprise information systems, it has been common to adopt a waterfall (WF)-type development method due to its adaptability to large-scale projects, high reliability, high efficiency in production, high estimation accuracy, and the like. Meanwhile, in recent years, the agile-type development method that repeats small releases is spreading as business environments change more intensely. For this reason, the development of a hybrid (HY)-type method that combines WF-type and agile-type development has attracted attention. Therefore, in this research, we report the result of examining the method that promotes rational development by considering the trade-off between cost reduction by simultaneous development of common objects as the overall optimality (the advantage of WF method) and early realization of value as local optimality (an advantage of agile method). For this purpose, we propose a method that achieves early realization of value and low cost by managing the relation between user stories and common objects in a matrix. Subsequently, we apply the proposed method to the basic design of a library information system and offer the results. In conclusion, we report cases where cost increases can be suppressed by delaying the value realization to some extent.
A Taxonomy of Modeling Techniques using Sketch-Based Interfaces

Traditional user interfaces in modeling have followed the WIMP (Window, Icon, Menu, Pointer) paradigm. While functional and powerful, they can also be cumbersome and daunting to a novice user; creating a complex model requires much expertise and effort. A recent trend is toward more accessible and natural interfaces, which has lead to sketch-based interfaces for modeling (SBIM). The goal is to allow hand-drawn sketches to be used in the modeling process, from rough model creation through to ﬁne detail construction. Mapping 2D sketches to a 3D modeling operation is a difﬁcult and ambiguous task, so our categorization is based on how an SBIM application chooses to interpret a sketch, of which there are three primary methods: to create a 3D model, to add details to an existing model, or to deform and manipulate a model. In this STAR, we present a taxonomy of sketch-based interfaces focused on geometric modeling applications. The canonical and recent works are presented and classiﬁed, including techniques for sketch acquisition, ﬁltering, and interpretation. The report also includes a discussion of important challenges and open problems for researchers to tackle in the coming years.
Contribution of dissolved organic C to stream metabolism: a mesocosm study using 13C-enriched tree-tissue leachate

Abstract Dissolved organic C (DOC) is metabolically important in streams, but its contribution to ecosystem metabolism is not well known because it is a complex mixture of mostly unidentified molecules. The uptake of bioavailable DOC in White Clay Creek (WCC), a 3rd-order stream in Pennsylvania, was estimated from the results of an experiment using 13C-labeled tree-tissue leachate and streambed sediments in recirculating mesocosms. The contribution of DOC in transport to stream metabolism was estimated from measurements of 13C-DOC uptake, 12C-DOC concentrations, and diel changes in dissolved O2 in the mesocosms. Eighty percent (±5) of the DOC in the 13C-tree-tissue leachate was bioavailable and belonged to 1 of 2 distinct lability classes, readily and intermediately labile. These components made up 88% (±0.6) and 12% (±0.6), respectively, of the biodegradable DOC in the leachate. Uptake mass transfer coefficients for the readily and intermediately labile components were 55 (±24) μm/s and 2.6 (±0.13) μm/s, respectively. Based on our mesocosm measurements, DOC in transport could support 33 to 54% of the bacterial C demand and up to 51% of the community respiration in WCC. Extrapolation of our results to WCC indicates that readily and intermediately labile DOC similar in quality to the 13C-DOC would travel 175 and 3692 m downstream in WCC before being taken up by the sediments. These distances represent ∼7% and >150% of the length of the 3rd-order reach. Our results suggest that readily labile DOC is an important energy source at the reach scale, whereas intermediately labile DOC serves as an energy subsidy from upstream to downstream reaches.
Decreasing Oxidative Stress with Choline and Carnitine in Women

Objective: Fatty acid oxidation is predominantly a mitochondrial event, which is enhanced by dietary choline and carnitine supplementation resulting in extra reactive oxygen species (ROS) load. The objective was to assess oxidative stress level by thiobarbituric acid reactive substances [TBARS] in choline and carnitine supplemented healthy women before and after mild exercise. Methods: Nineteen free-living women completed the placebo control study in which choline and/or L-carnitine was orally taken for 21 days. Anthropometric measurements, dietary recall, exercise routine and blood samples were analyzed to determine body composition, nutrients intake, distance walked and biochemical markers related to oxidative stress. Results: TBARS were significantly lower in the groups supplemented with choline, carnitine or both and the mild exercise (walking) was not a deterrent in this effect of the supplements. Serum vitamin A and E concentrations were higher in the supplemented groups even though the consumption of these nutrients was not different among the groups. Conclusion: Choline and carnitine supplementation lowers lipid peroxidation, and promotes conservation of retinol and α-tocopherol in free-living women.
Families, children, migration and AIDS

Abstract Migration is very often a family affair, and often involves children, directly or indirectly. It may give rise to better quality of life for an entire family, or to bitter disappointment, and may also increase vulnerability to HIV and AIDS. This review, carried out for the Joint Learning Initiative on Children and AIDS, links the literature on “migration”, on “HIV and AIDS” and on “families”. Three themes are sketched: (1) As both HIV prevalence and circular migration increase, former migrant workers affected by AIDS may return to their families for care and support, especially at the end of life, often under crisis conditions. Families thus lose promising members, as well as sources of support. However, very little is known about the children of such migrants. (2) Following patterns of migration established for far different reasons, children may have to relocate to different places, sometimes over long distances, if their AIDS-affected parents can no longer care for them. They face the same adaptation challenges as other children who move, but complicated by loss of parent(s), AIDS stigma, and often poverty. (3) The issue of migrant families living with HIV has been studied to some extent, but mainly in developed countries with a long history of migration, and with little attention paid to the children in such families. Difficulties include involuntary separation from family members, isolation and lack of support, disclosure and planning for children's care should the parent(s) die and differences in treatment access within the same family. Numerous research and policy gaps are defined regarding the three themes, and a call is made for thinking about migration, families and AIDS to go beyond description to include resilience theory, and to go beyond prevention to include care.
Modular Common-Mode Fault Tolerant NMR

TMR (Triple Modular Redundancy) is the most widely used Redundancy Technique in digital circuits. TMR hides the fault before spreading it through the rest of the system. In this paper, we propose a modular common-mode fault tolerating NMR (N Modular Redundancy) system capable of tolerating permanent, transient and intermittent faults that also indicates the number of modules that are faulty in the system, generally this later feature uncommon in existing techniques. It can also tolerate compensating module failures. It utilizes a word voter instead of conventional bit-bybit voter. The proposed modular design is valid for NMR and is demonstrated for 3MR. To the best of our knowledge, no single technique or design exists having all these features. Keywords—Availability, Common mode failure, Compensating module failure, Data integrity, Redundancy, Stuck-at-faults, TMR. Acronyms. AVTMR: All Voting TMR F: Fault condition FIM: Fault Injection Mechanism FIOM: Fault Indicating Output Module FTM: Fault Tolerant Module MCFTNMR: Modular Common-mode Fault Tolerant NMR M1, M2, M3: Input Modules NF: No Fault condition NMR: NModular Redundancy TMR: Triple Modular Redundancy XORM: XOR Module
Skin Colour-Based Face Detection in Colour Images

We propose in this work a method for detecting faces in colour images with complex backgrounds. The approach starts with the transformation of the image pixels from the RGB colour space to the chrominance space (YCbCr). Secondly, a Gaussian model is fitted on the transformed image in order to calculate the likelihood of skin for each pixel and to create a likelihood image. Thirdly, by thresholding the likelihood image, skin pixels are segmented to form a binary skin map, which contains the candidate face regions. Finally, a verification process is carried out to determine whether these candidate face regions are real faces or not.
Preconditioned Solution of State Gradient Constrained Elliptic Optimal Control Problems

Elliptic optimal control problems with pointwise state gradient constraints are considered. A quadratic penalty approach is employed together with a semismooth Newton iteration. Three different preconditioners are proposed and the ensuing spectral properties of the preconditioned linear Newton saddle-point systems are analyzed dependent on the penalty parameter. A new bound for the smallest positive eigenvalue is proved. Since the analysis is carried out in function space it will ensure mesh independent convergence behavior of suitable Krylov subspace methods such as Minres, also in discretized settings. A path-following strategy with a preconditioned inexact Newton solver is implemented and numerical results are provided.
Intelligence and the Mortality Difference by Education: Selection or mediation?

Large differences in mortality rates across those with different levels of education are a well-established fact. This association between mortality and education may partly be explained by confounding factors, including intelligence. Intelligence may also be affected by education so that it becomes a mediating factor in the causal chain. In this paper we estimate the impact of education on mortality using inverse probability weighted (IPW) estimator, using either intelligence as a selection variable or as a mediating variable. We develop an IPW estimator to analyse the mediating effect in the context of survival models. Our estimates are based on administrative data, on men born in 1944-1947 who were examined for military service in the Netherlands between 1961-1965, linked to national death records. For these men we distinguish four education levels and we make pairwise comparisons. From the empirical analyses we conclude that the mortality differences observed by education are only attributable to education effects for high educated individuals. For low educated individuals the observed mortality gain is mainly attributable to differences in intelligence.
Effects of cold exposure on physiology, meat quality, and behavior of turkey hens and toms crated at transport density

Abstract The impact of cold exposure while crated at a density characteristic of transport (83 kg/m2) was assessed in 12‐wk‐old turkey hens and 16‐wk‐old toms. Turkeys (72 toms, 72 hens) were randomly divided into 3 male and 3 female groups: 2 moderate 20°C groups with either 30% or 80% RH and a cold group exposed to ‐18°C, with uncontrolled, high RH. Groups of 8 birds (one replicate unit) were observed in a climate‐controlled chamber for 8 h prior to slaughter. Core body temperature (CBT), live shrink, heterophil‐lymphocyte ratio (HLR), and change in blood glucose levels were assessed; meat quality measures included thigh and breast muscle pH and L*, a*, and b* color values. Significance was declared at P ≤ 0.05. Live shrink in hens exposed to ‐18°C (2.8%) was greater (P = 0.001) than those in the 20°C treatments (1.5%). CBT in hens had a tendency to decrease (P = 0.070); no differences in &Dgr; blood glucose or HLR were detected. Thigh pH was higher in the ‐18°C treatment (hens: 6.39; toms: 6.08) than in both 20°C groups. Color values (L*, a*, and b*) were measured 27 h postmortem. In the ‐18°C exposed hens, breast L* values were lower, and thigh a* and breast b* values were higher than in both 20°C treatments. No differences were detected in live shrink, CBT, HLR, or color values among toms. Behavior differences were noted between treatments; more time was spent huddling, shivering, preening, and with feathers ptiloerected in cold‐exposed turkeys. Generally, cold exposure resulted in higher live shrink, darker meat with greater redness, and a tendency for CBT and blood glucose to decrease, with larger male turkeys experiencing fewer changes.