Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of habitat fragmentation on the genetic diversity and differentiation of Dendrolimus punctatus (Lepidoptera: Lasiocampidae) in Thousand Island Lake, China, based on mitochondrial COI gene sequences

Abstract Thousand Island Lake (TIL) is a typical fragmented landscape and an ideal model to study ecological effects of fragmentation. Partial fragments of the mitochondrial cytochrome oxidase subunit I gene of 23 island populations of Dendrolimus punctatus in TIL were sequenced, 141 haplotypes being identified. The number of haplotypes increased significantly with the increase in island area and shape index, whereas no significant correlation was detected between three island attributes (area, shape and isolation) and haplotype diversity. However, the correlation with number of haplotypes was no longer significant when the ‘outlier’ island JSD (the largest island) was not included. Additionally, we found no significant relationship between geographic distance and genetic distance. Geographic isolation did not obstruct the gene flow among D. punctatus populations, which might be because of the high dispersal capacity of this pine moth. Fragmentation resulted in the conversion of large and continuous habitats into isolated, small and insular patches, which was the primary effect on the genetic diversity of D. punctatus in TIL. The conclusion to emphasize from our research is that habitat fragmentation reduced the biological genetic diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection.
Bioinformatic analysis and identification of potential prognostic microRNAs and mRNAs in thyroid cancer

Thyroid cancer is one of the most common endocrine malignancies. Multiple evidences revealed that a large number of microRNAs and mRNAs were abnormally expressed in thyroid cancer tissues. These microRNAs and mRNAs play important roles in tumorigenesis. In the present study, we identified 72 microRNAs and 1,766 mRNAs differentially expressed between thyroid cancer tissues and normal thyroid tissues and evaluated their prognostic values using Kaplan-Meier survival curves by log-rank test. Seven microRNAs (miR-146b, miR-184, miR-767, miR-6730, miR-6860, miR-196a-2 and miR-509-3) were associated with the overall survival. Among them, three microRNAs were linked with six differentially expressed mRNAs (miR-767 was predicted to target COL10A1, PLAG1 and PPP1R1C; miR-146b was predicted to target MMP16; miR-196a-2 was predicted to target SYT9). To identify the key genes in the protein-protein interaction network , we screened out the top 10 hub genes (NPY, NMU, KNG1, LPAR5, CCR3, SST, PPY, GABBR2, ADCY8 and SAA1) with higher degrees. Only LPAR5 was associated with the overall survival. Multivariate analysis demonstrated that miR-184, miR-146b, miR-509-3 and LPAR5 were an independent risk factors for prognosis. Our results of the present study identified a series of prognostic microRNAs and mRNAs that have the potential to be the targets for treatment of thyroid cancer.
Structural and immunologic correlates of chemically stabilized HIV-1 envelope glycoproteins

Inducing broad spectrum neutralizing antibodies against challenging pathogens such as HIV-1 is a major vaccine design goal, but may be hindered by conformational instability within viral envelope glycoproteins (Env). Chemical cross-linking is widely used for vaccine antigen stabilization, but how this process affects structure, antigenicity and immunogenicity is poorly understood and its use remains entirely empirical. We have solved the first cryo-EM structure of a cross-linked vaccine antigen. The 4.2 Å structure of HIV-1 BG505 SOSIP soluble recombinant Env in complex with a CD4 binding site-specific broadly neutralizing antibody (bNAb) Fab fragment reveals how cross-linking affects key properties of the trimer. We observed density corresponding to highly specific glutaraldehyde (GLA) cross-links between gp120 monomers at the trimer apex and between gp120 and gp41 at the trimer interface that had strikingly little impact on overall trimer conformation, but critically enhanced trimer stability and improved Env antigenicity. Cross-links were also observed within gp120 at sites associated with the N241/N289 glycan hole that locally modified trimer antigenicity. In immunogenicity studies, the neutralizing antibody response to cross-linked trimers showed modest but significantly greater breadth against a global panel of difficult-to-neutralize Tier-2 heterologous viruses. Moreover, the specificity of autologous Tier-2 neutralization was modified away from the N241/N289 glycan hole, implying a novel specificity. Finally, we have investigated for the first time T helper cell responses to next-generation soluble trimers, and report on vaccine-relevant immunodominant responses to epitopes within BG505 that are modified by cross-linking. Elucidation of the structural correlates of a cross-linked viral glycoprotein will allow more rational use of this methodology for vaccine design, and reveals a strategy with promise for eliciting neutralizing antibodies needed for an effective HIV-1 vaccine.
Two-part models with stochastic processes for modelling longitudinal semicontinuous data: Computationally efficient inference and modelling the overall marginal mean

Several researchers have described two-part models with patient-specific stochastic processes for analysing longitudinal semicontinuous data. In theory, such models can offer greater flexibility than the standard two-part model with patient-specific random effects. However, in practice, the high dimensional integrations involved in the marginal likelihood (i.e. integrated over the stochastic processes) significantly complicates model fitting. Thus, non-standard computationally intensive procedures based on simulating the marginal likelihood have so far only been proposed. In this paper, we describe an efficient method of implementation by demonstrating how the high dimensional integrations involved in the marginal likelihood can be computed efficiently. Specifically, by using a property of the multivariate normal distribution and the standard marginal cumulative distribution function identity, we transform the marginal likelihood so that the high dimensional integrations are contained in the cumulative distribution function of a multivariate normal distribution, which can then be efficiently evaluated. Hence, maximum likelihood estimation can be used to obtain parameter estimates and asymptotic standard errors (from the observed information matrix) of model parameters. We describe our proposed efficient implementation procedure for the standard two-part model parameterisation and when it is of interest to directly model the overall marginal mean. The methodology is applied on a psoriatic arthritis data set concerning functional disability.
Agent based Model for Estimating HEVs Market: Focusing on the Case of Korea

In this article, I have studied the impact of vehicle prices, subsidies/penalties and tax incentives that affect the hybrid car market penetration in Korea. I have adopted an agent based modelling to analyse dynamic interaction between market participants. To derive the analytical results close to the current, realistic context of Korea, I have used real statistical data from government agencies and private institutions. The analysis results show that the investigated factors affect consumer-purchase. Especially, vehicle price change has highly significant influence on the market share of hybrid electric vehicles (HEVs) in Korea. Subsidy/penalty policy of Korea turns out to have rather less effect on HEV penetration. Furthermore, unlike the research findings for other countries, fuel price changes do not nearly affect the penetration rate.
Are We Making Progress in the Treatment of Neuroendocrine Tumors

Introduction The past decade has been remarkably productive in the history of neuroendocrine tumor (NET) research. Since 2009, results of 9 prospective phase III studies have been published, 7 of which met their primary endpoint (Table). These studies have dramatically altered the treatment landscape. The field of NET research, formerly dominated by anecdotal information, is now guided by principles of evidence-based medicine. When considering these innovations, it is important to recognize that NETs are a highly diverse family of neoplasms that can be categorized using multiple criteria. These include primary site (eg, small intestinal, pancreatic, colorectal, or bronchopulmonary), tumor grade (low, intermediate, and high), morphologic differentiation, hormonal output (functioning or nonfunctioning), extent of disease (localized, liver-dominant, or widely metastatic), and somatostatin receptor expression. While some therapies have been studied in broad categories of NETs, others have been designed to target very specific populations. The somatostatin analogs (SSAs) octreotide and lanreotide remain the cornerstone treatment for most well-differentiated, somatostatin-receptor–expressing metastatic NETs. Initially designed to palliate hormonal symptoms such as flushing and diarrhea associated with the carcinoid syndrome, both SSAs were subsequently found to inhibit tumor growth. This property, also known as the “antiproliferative effect” of SSAs, was demonstrated in 2 landmark studies: the PROMID study, which randomized patients with well-differentiated midgut NETs to receive octreotide long-acting release (LAR) versus placebo, and the CLARINET study, which evaluated lanreotide versus placebo in a more heterogeneous population of patients with nonfunctioning enteropancreatic NETs. In this review, we will focus on subsequent lines of therapy: mammalian target of rapamycin (mTOR) inhibition, using everolimus; antiangiogenic therapy, with a focus on sunitinib and bevacizumab; peptide receptor radiotherapy, using yttriumand lutetium-labeled somatostatin analogs; temozolomide-based cytotoxic chemotherapy; and telotristat, a novel serotonin synthesis inhibitor. Although liver-directed therapy remains highly important for patients with liver-dominant metastases, it is outside the scope of this review.
Cultural and Contextual Adaptation of an eHealth Intervention for Youth Receiving Services for First-Episode Psychosis: Adaptation Framework and Protocol for Horyzons-Canada Phase 1

Background eHealth interventions have the potential to address challenges related to access, service engagement, and continuity of care in the delivery of mental health services. However, the initial development and evaluation of such interventions can require substantive amounts of financial and human resource investments to bring them to scale. Therefore, it may be warranted to pay greater attention to policy, services, and research with respect to eHealth platforms that have the potential to be adapted for use across settings. Yet, limited attention has been placed on the methods and processes for adapting eHealth interventions to improve their applicability across cultural, geographical, and contextual boundaries. Objective In this paper, we describe an adaptation framework and protocol to adapt an eHealth intervention designed to promote recovery and prevent relapses in youth receiving specialized services for first-episode psychosis. The Web-based platform, called Horyzons, was initially developed and tested in Australia and is now being prepared for evaluation in Canada. Methods Service users and service providers from 2 specialized early intervention programs for first-episode psychosis located in different provinces will explore a beta-version of the eHealth intervention through focus group discussions and extended personal explorations to identify the need for, and content of contextual and cultural adaptations. An iterative consultation process will then take place with service providers and users to develop and assess platform adaptations in preparation for a pilot study with a live version of the platform. Results Data collection was completed in August 2017, and analysis and adaptation are in process. The first results of the study will be submitted for publication in 2018 and will provide preliminary insights into the acceptability of the Web-based platform (eg, perceived use and perceived usefulness) from service provider and service user perspectives. The project will also provide knowledge about the adaptations and process needed to prepare the platform for evaluation in Canada. Conclusions This study contributes to an important gap in the literature pertaining to the specific principles, methods, and steps involved in adapting eHealth interventions for implementation and evaluation across a diverse range of cultural, geographical, and health care settings.
Draft Genome Sequence of “Candidatus Phycosocius bacilliformis,” an Alphaproteobacterial Ectosymbiont of the Hydrocarbon-Producing Green Alga Botryococcus braunii

ABSTRACT “Candidatus Phycosocius bacilliformis” is an alphaproteobacterial ectosymbiont of the hydrocarbon-producing green alga Botryococcus braunii. We sequenced the whole genome of “Ca. P. bacilliformis” BOTRYCO-2, isolated from a two-membered culture with B. braunii. The genome contains approximately 3.3 Mb, with an average G+C content of 56.91% and 3,125 predicted protein-coding genes.
Long-haul DWDM transmission systems employing optical phase conjugation

In this paper, we review the recent progress in transmission experiments by employing optical phase conjugation (OPC) for the compensation of chromatic dispersion and nonlinear impairments. OPC is realized with difference frequency generation (DFG) in a periodically poled lithium-niobate (PPLN) waveguide, for transparent wavelength-division multiplexed (WDM) operation with high conversion efficiency. We discuss extensively the principle behind optical phase conjugation and the realization of a polarization independent OPC subsystem. Using OPC for chromatic dispersion compensation WDM 40-Gb/s long-haul transmission is described. As well, transmission employing both mixed data rates and mixed modulation formats is discussed. No significant nonlinear impairments are observed from the nonperiodic dispersion map used in these experiments. The compensation of intrachannel nonlinear impairments by OPC is described for WDM carrier-suppressed return-to-zero (CSRZ) transmission. In this experiment, a 50% increase in transmission reach is obtained by adding an OPC unit to a transmission line using dispersion compensating fiber (DCF) for dispersion compensation. Furthermore, the compensation of impairments due to nonlinear phase noise is reviewed. An in-depth analysis is conducted on what performance improvement is to be expected for various OPC configurations and a proof-of-principle experiment is described showing over 4-dB improvement in Q-factor due to compensation of nonlinear impairments resulting from nonlinear phase noise. Finally, an ultralong-haul WDM transmission of 22times20-Gb/s return-to-zero differential quadrature phase-shift keying (RZ-DQPSK) is discussed showing that OPC can compensate for chromatic dispersion, as well as self-phase modulation (SPM) induced nonlinear impairments, such as nonlinear phase noise. Compared to a "conventional" transmission link using DCF for dispersion compensation, a 44% increase in transmission reach is obtained when OPC is employed. In this experiment, we show the feasibility of using only one polarization-independent PPLN subsystem to compensate for an accumulated chromatic dispersion of over 160 000 ps/nm
Characteristics and management of patients with inflammatory bowel disease between a secondary and tertiary hospitals: a propensity score analysis

Background/Aims This study aimed to compare the clinical characteristics and management patterns of inflammatory bowel disease (IBD) patients in a secondary hospital (SH) with those in tertiary referral centers (TRC). Methods Data from IBD patients in SH and 2 TRCs were retrospectively reviewed. The cumulative thiopurine use rate was compared between hospitals after controlling for different baseline characteristics using propensity score matching. Results Among the total of 447 patients with IBD, 178 Crohn's disease (CD) and 269 ulcerative colitis (UC) patients were included. Regarding initial CD symptoms, patients from SH were more likely to show perianal symptoms, such as anal pain or discharge (56.6% vs. 34.3%, P=0.003), whereas those from TRCs more often had luminal symptoms, such as abdominal pain (54.9% vs. 17.1%, P<0.001), diarrhea (44.1% vs. 18.4%, P<0.001), and body weight loss (9.8% vs. 1.3%, P=0.025). Complicating behaviors, such as stricturing and penetrating, were significantly higher in TRCs, while perianal disease was more common in SH. Ileal location was more frequently observed in TRCs. For UC, SH had a more limited extent of disease (proctitis 58.8% vs. 21.2%, P<0.001). The cumulative azathioprine use rate in SH was significantly lower than that in TRCs in both CD and UC patients after controlling for disease behavior, location, and perianal disease of CD and extent of UC. Conclusions The clinical characteristics and management of the IBD patients in SH were substantially different from those in TRCs. Thiopurine treatment was less commonly used for SH patients.
Mitochondrial-DNA Phylogenetic Information and the Reconstruction of Human Population History: The South American Case

ABSTRACT Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history. We analyzed six data sets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), Control plus cytochrome b (cytb), and cytb plus 12S plus 16S. The amount of information in each data set was estimated employing several site-by-site and haplotype-based statistics, distances among sequences, neighbor-joining trees, distances among the estimated trees, Bayesian skyline plots, and phylogenetic informativeness profiles. The different mtDNA data sets have different amounts of information to reconstruct demographic events and phylogenetic trees with confidence. Whereas HVRI is not suitable for phylogenetic reconstruction of ancient clades, this region, as well as the Control data set, displays information for the demographic reconstruction during the Holocene period, probably because of the high rate of mutation of these regions. As expected, the Complete mtDNA and Coding data sets, displaying slower rates of mutation, present suitable information to estimate the founding subhaplogroups that populated South America and for the reconstruction of ancient demographic events. Our results point out the importance of evaluating the utility of different DNA regions to respond to different questions and problems in the human population studies, mainly considering the time scale of the phenomenon and the informativeness of the molecular region in a particular geographical area.
Effects of yogurt and bifidobacteria supplementation on the colonic microbiota in lactose‐intolerant subjects

Aims: Colonic metabolism of lactose may play a role in lactose intolerance. We investigated whether a 2‐week supplementation of Bifidobacterium longum (in capsules) and a yogurt enriched with Bifidobacterium animalis could modify the composition and metabolic activities of the colonic microbiota in 11 Chinese lactose‐intolerant subjects.
Protective factors and risk factors

Dyadic work relationships are fundamental to effective organizing and are a means by which individuals find meaning at work. Such relationships may contain latent competencies with the potential to infuse the dyad with purpose. Meaningful dyadic relationships depend on the dyad’s ability to be resilient to within-dyad adversity. Our conceptual analysis examines how interpersonal interactions emerge to dyad-level phenomena in the wake of such adversity. We introduce dyadic resilience, detail the process by which it emerges, identify protective factors and risk factors of dyadic resilience, and posit that the emergence of dyadic resilience influences dyadic thriving over time.
Using machine learning for real-time estimates of snow water equivalent in the watersheds of Afghanistan

Abstract. In the mountains, snowmelt often provides most of the runoff. Operational estimates use imagery from optical and passive microwave sensors, but each has its limitations. An accurate approach, which we validate in Afghanistan and the Sierra Nevada USA, reconstructs spatially distributed snow water equivalent (SWE) by calculating snowmelt backward from a remotely sensed date of disappearance. However, reconstructed SWE estimates are available only retrospectively; they do not provide a forecast. To estimate SWE throughout the snowmelt season, we consider physiographic and remotely sensed information as predictors and reconstructed SWE as the target. The period of analysis matches the AMSR-E radiometer's lifetime from 2003 to 2011, for the months of April through June. The spatial resolution of the predictions is 3.125 km, to match the resolution of a microwave brightness temperature product. Two machine learning techniques – bagged regression trees and feed-forward neural networks – produced similar mean results, with 0–14 % bias and 46–48 mm RMSE on average. Nash–Sutcliffe efficiencies averaged 0.68 for all years. Daily SWE climatology and fractional snow-covered area are the most important predictors. We conclude that these methods can accurately estimate SWE during the snow season in remote mountains, and thereby provide an independent estimate to forecast runoff and validate other methods to assess the snow resource.
Genetic rearrangements, hotspot mutations, and microRNA expression in the progression of metastatic adenoid cystic carcinoma of the salivary gland

Adenoid cystic carcinoma (ACC) is among the most common salivary gland malignancies, and is notorious for its unpredictable clinical course with frequent local recurrences and metastatic spread. However, the molecular mechanisms for metastatic spread are poorly understood. This malignancy is known to frequently harbor gene fusions involving MYB, MYBL1, and NFIB, and to have a low mutational burden. Most studies have focused on primary tumors to understand the biology of ACC, but this has not revealed a genetic cause for metastatic dissemination in the majority of cases. Hence, other molecular mechanisms are likely to be involved. Here, we characterize the genetic and microRNA expressional landscape of primary ACC and corresponding metastatic lesions from 11 patients. FISH demonstrated preservation of MYB aberrations between primary tumors and metastases, and targeted next-generation sequencing identified mutations exclusive for the metastatic lesions in 3/11 cases (27.3%). Global microRNA profiling identified several differentially expressed miRNAs between primary ACC and metastases as compared to normal salivary gland tissue. Interestingly, individual tumor pairs differed in miRNA profile, but there was no general difference between primary ACCs and metastases. Collectively, we show that MYB and NFIB aberrations are consistently preserved in ACC metastatic lesions, and that additional mutations included in the 50-gene hotspot panel used are infrequently acquired by the metastatic lesions. In contrast, tumor pairs differ in microRNA expression and our data suggest that they are heterogeneous according to their microRNA profile. This adds an additional layer to the complex process of ACC metastatic spread.