Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitation of Targetable Somatic Mutations Among Patients Evaluated by a Personalized Medicine Clinical Service: Considerations for Off‐Label Drug Use

Moffitt Cancer Center's Personalized Medicine Clinical Service (PMCS) reviews somatic next‐generation sequencing (NGS) assay results, provides interpretations, and identifies potential therapeutic options. The number of individuals reviewed by our clinical service who are eligible for on‐label or off‐label drug therapy based on genetic test results has previously not been quantitated. We determined the number of patients harboring an actionable mutation that would qualify a patient for an on‐label drug or consideration for off‐label drug treatment.
Stability and error estimates of BV solutions to the Abel inverse problem

Reconstructing images from ill-posed inverse problems often utilizes total variation regularization in order to recover discontinuities in the data while also removing noise and other artifacts. Total variation regularization has been successful in recovering images for (noisy) Abel transformed data, where object boundaries and data support will lead to sharp edges in the reconstructed image. In this work, we analyze the behavior of solutions to the Abel inverse problem, deriving a priori estimates on the recovery. In particular, we provide L2-stability bounds on solutions to the Abel inverse problem. These bounds yield error estimates on images reconstructed from a proposed total variation regularized minimization problem.
A Neighbor-Based Probabilistic Broadcast Protocol for Data Dissemination in Mobile IoT Networks

The recent trend of implementing Internet of Things (IoT) applications is to transmit sensing data to a powerful data center, and try to discover the valuable knowledge behind ``Big Data'' by various intelligent but resource-consuming algorithms. However, from the discussion with some industrial companies, it is understood that disseminating real-time sensing data to their nearby network-edge-applications directly would produce a more economical design and lower service latency for some important smart city applications. Therefore, this paper proposes an efficient broadcast protocol to disseminate data in mobile IoT networks. The proposed protocol exploits the neighbor knowledge of mobile nodes to determine a rebroadcast delay that prioritizes different packet broadcasts according to their profits. An adaptive connectivity factor is also introduced to make the proposed protocol adaptive to the node density of different network parts. By combining the neighbor knowledge of nodes and adaptive connectivity factor, a reasonable probability is calculated to determine whether a packet should be rebroadcasted to other nodes, or be discarded to prevent redundant packet broadcast. Extensive simulation results have validated that this protocol can improve the success ratio of packet delivery by 13% ~ 28% with a similar end-to-end transmission delay and network overhead of the most state-of-art approaches.
Questionnaire for Evaluation of Masticatory Function Complete Denture Wearer.

The purpose of this study was to set up a questionnaire for evaluating the masticatory ability and the change of the masticatory ability of complete denture wearers. Twenty kinds of food were selected from Uchida's 100 foods and the masticatory ability and the change of masticatory ability of 145 complete denture wearers were scored.The following results were drawn from the data:1. The scores of the masticatory ability and the change of the masticatory ability obtained from chewing aspect of 20 foods were the same as the scores obtained from 100 foods.2. The masticatory scores were associated with the maximal bite force of the patients.3. The average score of the masticatory ability with new dentures was significantly higher than with present dentures.4. The scores of the change of the masticatory ability between the new denture and the present denture were associated with the scores of the masticatory ability of the present denture.
Risk factors and prognosis for recurrent primary sclerosing cholangitis after liver transplantation: a Nordic Multicentre Study

Abstract Objectives: The risk for recurrent primary sclerosing cholangitis (rPSC) after liver transplantation is associated with inflammatory bowel disease (IBD). We assessed the frequency of rPSC and studied risk factors for recurrent disease with special focus on IBD. We also evaluated the importance of rPSC for prognosis. Materials and methods: All liver transplanted PSC patients in the Nordic countries between 1984 and 2007 (n = 440), identified by the Nordic Liver Transplant Registry, were studied. Data were retrieved from patients' chart reviews. Multivariable Cox regression models were used to calculate risk factors for rPSC and death. Results: Of the 440 patients with a follow-up time after liver transplantation of 3743 patient years, rPSC was diagnosed in 19% (n = 85). Colectomy before liver transplantation was associated with a reduced risk of rPSC (HR 0.49; 95% CI, 0.26–0.94, p = 0.033). Neither high IBD activity nor presence of IBD flares before or after liver transplantation was associated with rPSC. Treatment with tacrolimus was an independent risk factor associated with increased risk for rPSC (HR, 1.81; 95% CI, 1.15–2.86, p = 0.010). The risk of dying or needing a re-transplantation after rPSC was increased in all age groups, but highest in patients transplanted before 40 years of age (HR 7.3; 95% CI, 4.1–12.8, p = 0.0001). Conclusions: This study confirms that colectomy before liver transplantation is associated with a decreased risk of rPSC. Inflammatory activity of IBD was not associated with the risk of rPSC. Tacrolimus was an independent risk factor for PSC recurrence and its use as first line immunosuppression in PSC needs further study.
Genetics of Type 2 Diabetes in U.S. Hispanic/Latino Individuals: Results From the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Few genome-wide association studies (GWAS) of type 2 diabetes (T2D) have been conducted in U.S. Hispanics/Latinos of diverse backgrounds who are disproportionately affected by diabetes. We conducted a GWAS in 2,499 T2D case subjects and 5,247 control subjects from six Hispanic/Latino background groups in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Our GWAS identified two known loci (TCF7L2 and KCNQ1) reaching genome-wide significance levels. Conditional analysis on known index single nucleotide polymorphisms (SNPs) indicated an additional independent signal at KCNQ1, represented by an African ancestry–specific variant, rs1049549 (odds ratio 1.49 [95% CI 1.27–1.75]). This association was consistent across Hispanic/Latino background groups and replicated in the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium. Among 80 previously known index SNPs at T2D loci, 66 SNPs showed consistency with the reported direction of associations and 14 SNPs significantly generalized to the HCHS/SOL. A genetic risk score based on these 80 index SNPs was significantly associated with T2D (odds ratio 1.07 [1.06–1.09] per risk allele), with a stronger effect observed in nonobese than in obese individuals. Our study identified a novel independent signal suggesting an African ancestry–specific allele at KCNQ1 for T2D. Associations between previously identified loci and T2D were generally shown in a large cohort of U.S. Hispanics/Latinos.
Achievements in biomimetic composite structures with fore-wing of beetle

In order to develop light-weight biological composite,a series of research on the fore-wing structures of beetles were conducted.The microstructures of the fore-wing and trabeculae of beetle were investigated through dissection of the fore_wings of the beetle,and their models were established.At the same time,two types of beetles are compared and the different structures of their fore_wings were made clear.Based on mechanical experiments and the analysis of the fore-wing structures of beetles,it is confirmed that there exist outstanding mechanical characteristics in the structures of fore-wing.Then with these achievements,a sandwich_like plate structure with high tenacity is proposed.
Individualized arrhythmia detection with ECG signals from wearable devices

Low cost pervasive electrocardiogram (ECG) monitors is changing how sinus arrhythmia are diagnosed among patients with mild symptoms. With the large amount of data generated from long-term monitoring, come new data science and analytical challenges. Although traditional rule-based detection algorithms still work on relatively short clinical quality ECG, they are not optimal for pervasive signals collected from wearable devices-they don't adapt to individual difference and assume accurate identification of ECG fiducial points. To overcome these short-comings of the rule-based methods, this paper introduces an arrhythmia detection approach for low quality pervasive ECG signals. To achieve the robustness needed, two techniques were applied. First, a set of ECG features with minimal reliance on fiducial point identification were selected. Next, the features were normalized using robust statistics to factors out baseline individual differences and clinically irrelevant temporal drift that is common in pervasive ECG. The proposed method was evaluated using pervasive ECG signals we collected, in combination with clinician validated ECG signals from Physiobank. Empirical evaluation confirms accuracy improvements of the proposed approach over the traditional clinical rules.
Landscape Level Variation in Tick Abundance Relative to Seasonal Migration in Red Deer

Partial migration is common among northern ungulates, typically involving an altitudinal movement for seasonally migratory individuals. The main driving force behind migration is the benefit of an extended period of access to newly emerged, high quality forage along the green up gradient with increasing altitude; termed the forage maturation hypothesis. Any other limiting factor spatially correlated with this gradient may provide extra benefits or costs to migration, without necessarily being the cause of it. A common ectoparasite on cervids in Europe is the sheep tick (Ixodes ricinus), but it has not been tested whether migration may lead to the spatial separation from these parasites and thus potentially provide an additional benefit to migration. Further, if there is questing of ticks in winter ranges in May before spring migration, deer migration may also play a role for the distribution of ticks. We quantified the abundance of questing sheep tick within winter and summer home ranges of migratory (n = 42) and resident red deer (Cervus elaphus) individuals (n = 32) in two populations in May and August 2009–2012. Consistent with predictions, there was markedly lower abundance of questing ticks in the summer areas of migrating red deer (0.6/20 m2), both when compared to the annual home range of resident deer (4.9/20 m2) and the winter home ranges of migrants (5.8/20 m2). The reduced abundances within summer home ranges of migrants were explained by lower abundance of ticks with increasing altitude and distance from the coast. The lower abundance of ticks in summer home ranges of migratory deer does not imply that ticks are the main driver of migration (being most likely the benefits expected from forage maturation), but it suggests that ticks may add to the value of migration in some ecosystems and that it may act to spread ticks long distances in the landscape.
Material Selection Considerations for Polymer Composite Structures in Naval Ship Applications

The flexibility in the material selection for polymer composite sandwich structures in naval ship applications provides opportunities to optimize properties for various requirements. However, this freedom comes with a price in terms of increased complexity. This study presents considerations in the material selection process based on experience from the development of the composite sandwich structure for the 73 m Visby Class Corvette.
The Plundering of Agriculture in Developing Countries

Industry has been the darling of development, certainly for the now-industrial countries, and more recently for the developing countries. Those with the reins of policy in developing countries decided that agriculture was impervious to price incentives, so they believed that taxing it would sacrifice little in output. Moreover, agricultural taxes were easy to administer and extremely attractive in countries with a thin tax base. Also, shifting scarce resources to industry was thought to be justified by agriculture's declining terms of trade and by the rising protection in industrial countries. This research asks two basic questions: Is agriculture really that unresponsive to price incentives? And can countries develop faster and at lower cost by taxing agriculture? The authors examined how price interventions affect agricultural growth and overall economic growth and they measured the income transfers that price interventions induced among agriculture, government, and the rest of the economy. To see whether controls on food prices helped the poor, they studied the effects of price interventions on the incomes of the rural and urban poor in the short- and long-run. To see whether the policies for the prices of agricultural commodities kept them stable, they separated the effects of those policies from the effects of other forces determining commodity prices. The findings of this study provide a solid base for prescribing agricultural price policy.
Collagenase Impacts the Quantity and Quality of Native Mesenchymal Stem/Stromal Cells Derived during Processing of Umbilical Cord Tissue

Enzymes are commonly used as a biochemical means to liberate cells from a host of tissues for use in in vitro studies and/or in vivo transplantations. However, very little understanding exists of the biological and functional effects that enzymes have on cells during the process of releasing the native cells from a given tissue. One specific reason for this is that no technology has existed as a nonenzymatic control to compare baseline biology and function for a given processed tissue. We have developed a sterile, onetime use, disposable system (referred to as the AuxoCell Processing System or AC:Px®) that allows for processing of solid tissue in a closed, standardized system using mechanical means to liberate cells without the need and/or use of any biochemical, enzymatic digestion. In this report, for the first time, we directly compare the cellular outputs derived from processing the same umbilical cord tissue (UCT) in the presence and absence of collagenase. In the presence of collagenase, we observed on average, approximately a 2.7-fold reduction in native mesenchymal stem/stromal cell (MSC) yields and a reduction in MSC-specific markers CD90, CD29, CD105, CD73, CD44, CD36, CD49b, CD49a, CD146, CD295, and CD166 and in endothelial marker CD31. These data directly exhibit that the use of collagenase to process UCT to release cells impacts cell recovery with respect to number and cell surface marker expression and, hence, could affect the in vivo function of the recovered native cellular population.
Adeno-Associated Virus (AAV) gene therapy for cystic fibrosis: current barriers and recent developments

ABSTRACT Introduction: Since the cystic fibrosis (CF) gene was discovered in 1989, researchers have worked to develop a gene therapy. One of the most promising and enduring vectors is the AAV, which has been shown to be safe. In particular, several clinical trials have been conducted with AAV serotype 2. All of them detected viral genomes, but identification of mRNA transduction was not consistent; clinical outcomes in Phase II studies were also inconsistent. The lack of a positive outcome has been attributed to a less-than-efficient viral infection by AAV2, a weak transgene promoter and the host immune response to the vector. Areas covered: Herein, the authors focus on AAV gene therapy for CF, evaluating past experience with this approach and identifying ways forward, based on the progress that has already been made in identifying and overcoming the limitations of AAV gene therapy. Expert opinion: Such progress makes it clear that this is an opportune time to push forward toward the development of a gene therapy for CF. Drugs to treat the basic defect in CF represent a remarkable advance but cannot treat a significant cohort of patients with rare mutations. Thus, there is a critical need to develop a gene therapy for those individuals.
Major Transcriptome Reprogramming Underlies Floral Mimicry Induced by the Rust Fungus Puccinia monoica in Boechera stricta

Pucciniamonoica is a spectacular plant parasitic rust fungus that triggers the formation of flower-like structures (pseudoflowers) in its Brassicaceae host plant Boechera stricta . Pseudoflowers mimic in shape, color, nectar and scent co-occurring and unrelated flowers such as buttercups. They act to attract insects thereby aiding spore dispersal and sexual reproduction of the rust fungus. Although much ecological research has been performed on P . monoica -induced pseudoflowers, this system has yet to be investigated at the molecular or genomic level. To date, the molecular alterations underlying the development of pseudoflowers and the genes involved have not been described. To address this, we performed gene expression profiling to reveal 256 plant biological processes that are significantly altered in pseudoflowers. Among these biological processes, plant genes involved in cell fate specification, regulation of transcription, reproduction, floral organ development, anthocyanin (major floral pigments) and terpenoid biosynthesis (major floral volatile compounds) were down-regulated in pseudoflowers. In contrast, plant genes involved in shoot, cotyledon and leaf development, carbohydrate transport, wax biosynthesis, cutin transport and L-phenylalanine metabolism (pathway that results in phenylethanol and phenylacetaldehyde volatile production) were up-regulated. These findings point to an extensive reprogramming of host genes by the rust pathogen to induce floral mimicry. We also highlight 31 differentially regulated plant genes that are enriched in the biological processes mentioned above, and are potentially involved in the formation of pseudoflowers. This work illustrates the complex perturbations induced by rust pathogens in their host plants, and provides a starting point for understanding the molecular mechanisms of pathogen-induced floral mimicry.
Statistical Methods for Research Workers

THE volume under review is the fourth edition, revised and enlarged, of a “Biological Monograph” first published in 1925. As the editors point out, “Conspicuous progress is now being seen in the field of general physiology, of experimental biology and in the application of biological principles to economic problems”. This involves the analysis of large masses of data by statistical methods, in the process of which, solutions to many complex problems have to be sought. Stimulus is thus given to purely mathematical researches, upon which the methods dealt with in the book are based. The aim of the author is to apply accurate tests to practical data by systematically attacking small sample problems on their merits. No attempt is therefore made to prove rigorously the various propositions upon which the theory rests; for these the reader is referred to an excellent bibliography at the end.Statistical Methods for Research Workers.By Dr. R. A. Fisher. Fourth edition, revised and enlarged. Pp. xiv + 307. (Edinburgh and London: Oliver and Boyd, 1932.) 15s. net.
Malaysian to German sign language statistical machine translation using Markov chain and search algorithms

Sign language has shown advancement indication results in the last decade of years. Research in the area of sign language has been done but mostly focuses in signer independent schemas consists of sign language and video. Unfortunately, research of sign language to translate one sign language to another sign language is infrequently. The research contributes to Malaysian to German sign language statistical machine translation for hearing impaired people. Markov chain and search algorithms are used to apply the process of translation from Malaysian to German sign language and vice versa. The corpus data are used for testing statistical machine translation around 10.000. A binary search and linear search algorithm in cooperation with a Markov chain are used to apply the process of translation. An output of execution time between 2 models of algorithms has been explored. The accuracy of the binary search algorithm is better than linear search algorithm when using for translation.
Diagnostic significance of serum periostin in eosinophilic chronic sinusitis with nasal polyps

Abstract Objectives: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a heterogeneous disease. Eosinophilic CRSwNP (ENP) exhibits a strong tendency for recurrence after surgery. Given that the treatment strategy of ENP differs from that of non-eosinophilic CRSwNP (nENP), clinical diagnostic criteria that distinguish ENP from nENP are needed. Methods: In total, 94 CRSwNP patients were enrolled in the cohort. Factors associated with ENP were determined with regression analysis, and optimal cutoff points of the predictors were determined by a receiver operating characteristic curve. Results: Serum periostin levels, blood eosinophils and basophils counts significantly differed between ENP and nENP. A combination of the cut-off values for the three predictors, including absolute blood eosinophil and basophil counts, yielded a sensitivity of 79.2% and 70.8%, and a specificity of 84.8% and 73.9%, respectively. Serum periostin levels yielded a sensitivity of 72.9% and a specificity of 60.9% for the diagnosis of ENP. The predicted probability of periostin in combination with blood eosinophils and basophils counts (AUC, 0.872) exhibited moderate accuracy. In addition, patients with ENP displayed an increased prevalence of smoking. Conclusions: Periostin in combination with blood eosinophils and basophils counts has the potential to better refine current CRSwNP phenotypes.