Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing the local consensus of trees

The inference of consensus from a set of evolutionary trees is a fundamental problem in a number of fields such as biology and historical linguistics, and many models for inferring this consensus have been proposed. In this paper we present a model for deriving what we call a local consensus tree T from a set of trees ${\cal T}$. The model we propose presumes a function f, called a total local consensus function, which determines for every triple A of species, the form that the local consensus tree should take on A. We show that all local consensus trees, when they exist, can be constructed in polynomial time and that many fundamental problems can be solved in linear time. We also consider partial local consensus functions and study optimization problems under this model. We present linear time algorithms for several variations. Finally we point out that the local consensus approach ties together many previous approaches to constructing consensus trees.
Association between TGFB3 and Nonsyndromic Cleft Lip with or Without Cleft Palate in a Chilean Population

Objective To assess the possible association between TGFB3 allele variants and nonsyndromic cleft lip with or without cleft palate in a Chilean population. Design In our study we used a case-parents trios design. The sample consisted of 150 unrelated trios ascertained through probands affected with nonsyndromic cleft lip with or without cleft palate. Three TGFB3 polymorphisms were analyzed (rs2268626, rs2268625, and rs3917201). An allele/haplotype transmission disequilibrium test was used to evaluate the possible genotype-phenotype association. Results An overtransmission from parents to affected progeny was observed for the A allele of rs3917201 (p = .03) and for the rs2268625-rs3917201 A-A haplotype (p = .022). A defect of transmission of rs2268625-rs3917201 G-G haplotype (p = .022) was observed also. Conclusions Allelic and haplotypic associations implicate a possible role of TGFB3 in nonsyndromic cleft lip with or without cleft palate in the Chilean population. Additional studies are needed in order to elucidate the possible mechanisms that can explain the role of TGFB3 genetic variants in the condition.
Passivity-based whole-body balancing for torque-controlled humanoid robots in multi-contact scenarios

This work presents a new control approach to multi-contact balancing for torque-controlled humanoid robots. The controller includes a non-strict task hierarchy, which allows the robot to use a subset of its end effectors for balancing while the remaining ones can be used for interacting with the environment. The controller creates a passive and compliant behavior for regulating the center of mass (CoM) location, hip orientation and the poses of each end effector assigned to the interaction task. This is achieved by applying a suitable wrench (force and torque) at each one of the end effectors used for interaction. The contact wrenches at the balancing end effectors are chosen such that the sum of the balancing and interaction wrenches produce the desired wrench at the CoM. The algorithm requires the solution of an optimization problem, which distributes the CoM wrench to the end effectors taking into account constraints for unilaterality, friction and position of the center of pressure. Furthermore, the feedback controller is combined with a feedforward control in order to improve performance while tracking a predefined trajectory, leading to a control structure similar to a PD+ control. The controller is evaluated in several experiments with the humanoid robot TORO.
Multimedia Animated Corrosion for Corrosion and Coating Metals Course

Multimedia Animation in teaching metal corrosion and plating course on the corrosion proses remains largely unused. There are many students who do not understand the corrosion process, despite having attended lectures. This study aims to discover the effect of Multimedia Animation on students achievement. This study applied a quasi-experimental method on two classes, consisting of a control class using image media and an experimental class using Multimedia Animation. Instruments used for measuring learning are pretest and posttest. So, are the learning results obtained by using Multimedia Animation better than those using image media? The results showed that the use of Multimedia Animation is better than the use of image media. Keywords—multimedia animation; teaching corrosion; plating course
Granulysin Delivered by Cytotoxic Cells Damages Endoplasmic Reticulum and Activates Caspase-7 in Target Cells

Granulysin is a human cytolytic molecule present in cytotoxic granules with perforin and granzymes. Recombinant 9-kDa granulysin kills a variety of microbes, including bacteria, yeast, fungi, and parasites, and induces apoptosis in tumor cells by causing intracellular calcium overload, mitochondrial damage, and activation of downstream caspases. Reasoning that granulysin delivered by cytotoxic cells may work in concert with other molecules, we crossed granulysin transgenic (GNLY+/−) mice onto perforin (perf)- or granzyme B (gzmb)-deficient mice to examine granulysin-mediated killing in a more physiologic whole-cell system. Splenocytes from these animals were activated in vitro with IL-15 to generate cytolytic T cells and NK cells. Cytotoxic cells expressing granulysin require perforin, but not granzyme B, to cause apoptosis of targets. Whereas granzyme B induces mitochondrial damage and activates caspases-3 and -9 in targets, cytotoxic cell-delivered granulysin induces endoplasmic reticulum stress and activates caspase-7 with no effect on mitochondria or caspases-3 and -9. In addition, recombinant granulysin and cell-delivered granulysin activate distinct apoptotic pathways in target cells. These findings suggest that cytotoxic cells have evolved multiple nonredundant cell death pathways, enabling host defense to counteract escape mechanisms employed by pathogens or tumor cells.
Testing causality in variance using multivariate GARCH models

les tests de causalite en variance dans des series temporelles multiples ont ete recemment proposes, qui se fondent sur les residus estimes a partir de modeles univaries. Bien que ces tests soient souvent utilises, on sait peu de chose sur leur puissance. Dans cette article, nous presentons une autre methode pratique, qui consiste a specifier un modele a volatilite multivariee, comme le GARCH multivarie (ou BEKK), et a construire un test de Wald de non-causalite en variance. Nous comparons la premiere approche a cette derniere pour tester la causalite en variance a la fois asymptotiquement et a distance finie. On montre que le test de Wald a de meilleures proprietes de puissance sous une sequence d'alternatives locales. De plus, nous montrons par simulation que le test de Wald est assez robuste a une mauvaise specification de la vraisemblance. Sous-estimer l'ordre du BEKK et negliger l'effet de levier potentiel en volatilite induit des pertes mineures mais la methode conserve son avantage en puissance par rapport a celle fondee sur les residus.
Optimizations Enabled by a Decoupled Front-End Architecture

In the pursuit of instruction-level parallelism, significant demands are placed on a processor's instruction delivery mechanism. Delivering the performance necessary to meet future processor execution targets requires that the performance of the instruction delivery mechanism scale with the execution core. Attaining these targets is a challenging task due to I-cache misses, branch mispredictions, and taken branches in the instruction stream. To counter these challenges, we present a fetch architecture that decouples the branch predictor from the instruction fetch unit. A Fetch Target Queue (FTQ) is inserted between the branch predictor and instruction cache. This allows the branch predictor to run far in advance of the address currently being fetched by the cache. The decoupling enables a number of architecture optimizations, including multilevel branch predictor design, fetch-directed instruction prefetching, and easier pipelining of the instruction cache. For the multilevel predictor, we show that it performs better than a single-level predictor, even when ignoring the effects of cycle-timing issues. We also examine the performance of fetch-directed instruction prefetching using a multilevel branch predictor and show that an average 19 percent speedup is achieved. In addition, we examine pipelining the instruction cache to achieve a faster cycle time for the processor pipeline and show that pipelining provides an average 27 percent speedup over not pipelining the instruction cache for the programs examined.
Recent Advances in Electrochemical Biosensors Based on Fullerene-C60 Nano-Structured Platforms

Nanotechnology is becoming increasingly important in the field of (bio)sensors. The performance and sensitivity of biosensors is greatly improved with the integration of nanomaterials into their construction. Since its first discovery, fullerene-C60 has been the object of extensive research. Its unique and favorable characteristics of easy chemical modification, conductivity, and electrochemical properties has led to its tremendous use in (bio)sensor applications. This paper provides a concise review of advances in fullerene-C60 research and its use as a nanomaterial for the development of biosensors. We examine the research work reported in the literature on the synthesis, functionalization, approaches to nanostructuring electrodes with fullerene, and outline some of the exciting applications in the field of (bio)sensing.
Grammatical Planning Units During Real-Time Sentence Production in Speakers With Agrammatic Aphasia and Healthy Speakers.

PURPOSE Grammatical encoding (GE) is impaired in agrammatic aphasia; however, the nature of such deficits remains unclear. We examined grammatical planning units during real-time sentence production in speakers with agrammatic aphasia and control speakers, testing two competing models of GE. We queried whether speakers with agrammatic aphasia produce sentences word by word without advanced planning or whether hierarchical syntactic structure (i.e., verb argument structure; VAS) is encoded as part of the advanced planning unit. METHOD Experiment 1 examined production of sentences with a predefined structure (i.e., "The A and the B are above the C") using eye tracking. Experiment 2 tested production of transitive and unaccusative sentences without a predefined sentence structure in a verb-priming study. RESULTS In Experiment 1, both speakers with agrammatic aphasia and young and age-matched control speakers used word-by-word strategies, selecting the first lemma (noun A) only prior to speech onset. However, in Experiment 2, unlike controls, speakers with agrammatic aphasia preplanned transitive and unaccusative sentences, encoding VAS before speech onset. CONCLUSIONS Speakers with agrammatic aphasia show incremental, word-by-word production for structurally simple sentences, requiring retrieval of multiple noun lemmas. However, when sentences involve functional (thematic to grammatical) structure building, advanced planning strategies (i.e., VAS encoding) are used. This early use of hierarchical syntactic information may provide a scaffold for impaired GE in agrammatism.
Frustratingly Easy Domain Adaptation

We describe an approach to domain adaptation that is appropriate exactly in the case when one has enough “target” data to do slightly better than just using only “source” data. Our approach is incredibly simple, easy to implement as a preprocessing step (10 lines of Perl! ) and outperforms stateof-the-art approaches on a range of datasets. Moreover, it is trivially extended to a multidomain adaptation problem, where one has data from a variety of different domains.
Comprehensive Genome Profiling of Single Sperm Cells by Multiple Annealing and Looping‐Based Amplification Cycles and Next‐Generation Sequencing from Carriers of Robertsonian Translocation

Robertsonian translocation (RT) is a common cause for male infertility, recurrent pregnancy loss, and birth defects. Studying meiotic recombination in RT‐carrier patients helps decipher the mechanism and improve the clinical management of infertility and birth defects caused by RT. Here we present a new method to study spermatogenesis on a single‐gamete basis from two RT carriers. By using a combined single‐cell whole‐genome amplification and sequencing protocol, we comprehensively profiled the chromosomal copy number of 88 single sperms from two RT‐carrier patients. With the profiled information, chromosomal aberrations were identified on a whole‐genome, per‐sperm basis. We found that the previously reported interchromosomal effect might not exist with RT carriers. It is suggested that single‐cell genome sequencing enables comprehensive chromosomal aneuploidy screening and provides a powerful tool for studying gamete generation from patients carrying chromosomal diseases.
Coordinated Beamforming With Relaxed Zero Forcing: The Sequential Orthogonal Projection Combining Method and Rate Control

In this paper, coordinated beamforming based on relaxed zero forcing (RZF) for transmitter-receiver pair multiple-input single-output (MISO) and multiple-input multiple-output (MIMO) interference channels is considered. In the RZF coordinated beamforming, conventional zero-forcing interference leakage constraints are relaxed so that some predetermined interference leakage to undesired receivers is allowed in order to increase the beam design space for larger rates than those of the zero-forcing (ZF) scheme or to make beam design feasible when ZF is impossible. In the MISO case, it is shown that the rate-maximizing beam vector under the RZF framework for a given set of interference leakage levels can be obtained by sequential orthogonal projection combining (SOPC). Based on this, exact and approximate closed-form solutions are provided in two-user and three-user cases, respectively, and an efficient beam design algorithm for RZF coordinated beamforming is provided in general cases. Furthermore, the rate control problem under the RZF framework is considered. A centralized approach and a distributed heuristic approach are proposed to control the position of the designed rate-tuple in the achievable rate region. Finally, the RZF framework is extended to MIMO interference channels by deriving a new lower bound on the rate of each user.
Bias-stress-stable solution-processed oxide thin film transistors.

We generated a novel amorphous oxide semiconductor thin film transistor (AOS-TFT) that has exellent bias-stress stability using solution-processed gallium tin zinc oxide (GSZO) layers as the channel. The cause of the resulting stable operation against the gate bias-stress was studied by comparing the TFT characteristics of the GSZO layer with a tin-doped ZnO (ZTO) layer that lacks gallium. By photoluminescence, X-ray photoelectron, and electron paramagnetic resonance spectroscopy, we found that the GSZO layer had a significantly lower oxygen vacancy, which act as trap sites, than did the ZTO film. The successful fabrication of a solution-processable GSZO layer reported here is the first step in realizing all-solution-processed transparent flexible transistors with air-stable, reproducible device characteristics.
Cost‐Effectiveness of Deep Brain Stimulation for Advanced Parkinson's Disease in the United States

Deep brain stimulation (DBS), which uses an implantable device to modulate brain activity, is clinically superior to medical therapy for treating advanced Parkinson's disease (PD). We studied the cost‐effectiveness of DBS in conjunction with medical therapy compared to best medical therapy (BMT) alone, using the latest clinical and cost data for the U.S. healthcare system.
Synoptic weather types in the south of South America and their relationship to daily rainfall in the core crop-producing region in Argentina

Introduction The Argentine Pampas Region extends over 600 000 km2 and is one of the most important crop-producing regions in the world (SAGPyA 2008) (Fig. 1(a), shaded rectangle). In this region, extreme rainfall events often occur and have a significant socio-economic impact. In Argentina, irrigation is very rarely used, and rainfall and its spatio-temporal variability are therefore crucial for successful harvests. Rainfall events depend, among other factors, on the largescale atmospheric fields. There are two main approaches in synoptic climatology to investigate the links between localscale environmental features and large-scale circulation Synoptic weather types in the south of South America and their relationship to daily rainfall in the core crop-producing region in Argentina
Metabolomics for Plant Improvement: Status and Prospects

Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
CO2 enhancement of forest productivity constrained by limited nitrogen availability

Stimulation of terrestrial plant production by rising CO2 concentration is projected to reduce the airborne fraction of anthropogenic CO2 emissions. Coupled climate–carbon cycle models are sensitive to this negative feedback on atmospheric CO2, but model projections are uncertain because of the expectation that feedbacks through the nitrogen (N) cycle will reduce this so-called CO2 fertilization effect. We assessed whether N limitation caused a reduced stimulation of net primary productivity (NPP) by elevated atmospheric CO2 concentration over 11 y in a free-air CO2 enrichment (FACE) experiment in a deciduous Liquidambar styraciflua (sweetgum) forest stand in Tennessee. During the first 6 y of the experiment, NPP was significantly enhanced in forest plots exposed to 550 ppm CO2 compared with NPP in plots in current ambient CO2, and this was a consistent and sustained response. However, the enhancement of NPP under elevated CO2 declined from 24% in 2001–2003 to 9% in 2008. Global analyses that assume a sustained CO2 fertilization effect are no longer supported by this FACE experiment. N budget analysis supports the premise that N availability was limiting to tree growth and declining over time —an expected consequence of stand development, which was exacerbated by elevated CO2. Leaf- and stand-level observations provide mechanistic evidence that declining N availability constrained the tree response to elevated CO2; these observations are consistent with stand-level model projections. This FACE experiment provides strong rationale and process understanding for incorporating N limitation and N feedback effects in ecosystem and global models used in climate change assessments.
Central compartment dissection for well differentiated thyroid cancer … and the band plays on

Purpose of reviewThe role of central compartment dissection in the surgical management of well differentiated thyroid cancer is controversial. Lack of high-quality prospective studies results in management decisions being based on expert opinions and weaker levels of evidence. The American Thyroid Association has recently revised its management guidelines with particular emphasis on this topic, and a separate working group has set out to define the surgical anatomy that encompasses this procedure. Recent findingsCentral compartment dissection comprises the removal of nodal tissue from the prelaryngeal, pretracheal and paratracheal compartments, with no role for berry-picking procedures. There is universal agreement that therapeutic nodal dissection should be performed in patients with metastatic disease detected either through preoperative imaging or during intraoperative evaluation of the central compartment, with either visual inspection or frozen-section pathology. In contrast, there may be limited benefit from routine prophylactic central compartment dissection, for either disease recurrence or survival outcomes. As such, it should be performed only in patients deemed high risk: larger tumors, extra-thyroidal extension or aggressive histologic subtypes. SummaryFuture studies should focus on identifying the subpopulation of patients who would most benefit from these procedures and spare low-risk patients from the unwanted complications.
Risk Factors for Chronic Kidney Disease among American Indians and Alaska Natives – Findings from the Kidney Early Evaluation Program

Background: American Indians and Alaska Natives (AIAN) have a high incidence of end-stage renal disease. Less is known about chronic kidney disease (CKD) among AIAN and whether risk factors differ for low estimated glomerular filtration rate (eGFR) versus albuminuria with a normal eGFR. Methods: Cross-sectional study examining the associations of age, sex, smoking, obesity, diabetes, hypertension, family history, and geographic region with CKD among a screened population of AIAN participants in the Kidney Early Evaluation Program from 2000 to 2006. CKD was defined by the presence of either a low eGFR, <60 ml/min/1.73 m2, or albuminuria, a urine albumin/creatinine ratio ≥30 mg/g. Results: The prevalence of any CKD was 29%, of low eGFR was 17%, and of albuminuria with a normal eGFR was 12%. Older age was the strongest predictor of low eGFR (61+ years OR 8.42, 95% CI 5.92–11.98), followed by hypertension (OR 2.38, 95% CI 1.74–3.26). In contrast, diabetes (OR 2.04, 95% CI 1.57–2.64) and hypertension (OR 2.63, 95% CI 1.93–3.59) were the only predictors of albuminuria among persons with a normal eGFR. Conclusion: The burden of CKD was high among this screened population of AIAN, and different risk factor patterns were associated with low eGFR and albuminuria. Innovative programs and longitudinal research are needed to address CKD among AIAN.