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Community inclusion is a human right for all people, including people with mental illness. It is also an important part of individualized support to enable people experiencing mental illness to live in their preferred communities and to recover. In Taiwan, no study has investigated the social experiences of healthcare professionals. To fill this knowledge gap and inform ongoing mental health system strengthening, this study examined the not-in-my-backyard (NIMBY) phenomenon observed while establishing community mental health clubhouses in Taiwan and corresponding experiences of community inclusion. Data were collected through semi-structured interviews of 16 purposively sampled frontline healthcare professionals from Taiwanese mental health clubhouses. Data were analyzed using qualitative content analysis. Two themes were identified: "NIMBY phenomenon: Community residents' resistance to clubhouses" and "Measures adopted by the clubhouse for community inclusion". Two categories with eleven subcategories emerged. The findings demonstrate the following conclusions. First, the NIMBY phenomenon is related to the stigmatization and discrimination faced by individuals with mental disorders in society. Second, in Asian societies, mental disorders are associated with a particular social and cultural context. Third, the fear and rejection of individuals with mental disorders deepen their social exclusion. Forth, community mental health clubhouse models employ seven strategic approaches to community inclusion, listed as follows: capacity building for individuals, direct interaction with the public through community activities, provision of community services, life skills training, repairing and managing neighborhood relationships, assisting individuals in obtaining community employment, and conducting social education for community residents. Clearly, we need to combat social exclusion of people with mental illness and promote inclusive and accessible services and systems across sectors.

Taiwanese community mental health facilities encounter opposition/resistance from residents, commonly known as "Not-In-My-Backyard" (NIMBYism). This study investigated NIMBYism during the establishment of such facilities and how they respond to such resistance. A qualitative study through semi-structured interviews was used to obtain purposively sampled data. Fifteen frontline healthcare professionals from community mental health facilities in Taiwan were interviewed individually, using an organizational analysis structure. Data were analyzed using qualitative content analysis. Two themes: "Reasons for Resident Resistance" and "Institutional Response Strategies", two categories, and 11 subcategories emerged. The findings demonstrated the following: (1) Reasons behind residents' resistance toward establishing community mental health facilities are diverse. (2) Communities lack understanding regarding people with mental disorders, leading to irrational beliefs. (3) Fear and negative perceptions toward people with mental disorders exist. (4) Strategies employed by the facilities include providing community services to foster amicable relationships, organizing community outreaches, training people with mental disorders within communities, nurturing neighborhood connections, establishing and sustaining friendships within communities, inviting residents to visit community mental health facilities or introducing the facilities to communities, and leveraging governmental support. The government should adopt regulations or laws to reduce discrimination, promote human rights, and legislate to demarcate the use of community land.

Only a small number of avian species inhabit salty environments. To understand how they adapted, we examined the evolution of kidney sizes, supraorbital salt glands (SSGs), and the utilization of salty habitats across 230 species spanning 25 avian orders. Phylogenetic analysis indicates that SSGs, large kidneys, and thriving in salty habitats emerged convergently in birds. Transition rate analysis reveals that species possessing SSGs and large kidneys tended to move from low-to high-salinity environments, while others moved in the opposite direction. However, habitat salinity also influenced kidney evolution; lineages residing in high-salinity environments tended to develop larger kidneys than those in low-salinity environments. Our findings suggest that SSGs and large kidneys may have evolved through adaptation to high salinity. Overall, habitat conditions and physiological traits influenced avian adaptation to salty environments in a reciprocal manner. These results shed the new light on the evolutionary mechanisms underlying functional diversity in birds., Competing Interests: None of the authors of this article have any affiliations with or involvement in any organization or entity with any financial or non-financial interest (such as patent or stock ownership, membership of a company board of directors, membership of an advisory board or committee for a company, and consultancy for or receipt of speaker’s fees from a company) in the subject matter or materials discussed in this article., (© 2024 The Authors.)

Psychological disorders have become more prevalent in the presence of modernization and societal changes. Community-based mental health is important in healthcare. Taiwan has passed the Mental Health Act, and county governments have established community-based mental healthcare centers. This study aimed to fill the research gap regarding the operational status of these centers. A qualitative study design using semi-structured interviews was used to obtain data from a purposive sample. Seventeen healthcare professionals who were front-line workers of a community-based mental healthcare center in Taiwan were interviewed individually. This study uses the organizational analysis structure as the research base. The data were analyzed using qualitative content analysis. The theme-"operational status and difficulties"-and two categories with twelve subcategories emerged. The findings demonstrate (1) unclear objectives and imprecisely defined roles, (2) incomplete services provided, an overly defined area, and ineffectiveness, (3) the central government lacking clear objectives and operational strategies, (4) the public being ignorant of mental diseases and the operation of the centers, and (5) the lack of local resources for mental and social welfare. The government should immediately form clear policies to improve community-based mental healthcare, clarify the structure and models, increase resources for the centers, and provide direct services., Competing Interests: The authors declare no conflicts of interest.

Objective: This study aims to investigate the variations in fatigue and sleep disturbances among female patients with advanced lung cancer (ALC) and advanced breast cancer (ABC) during chemotherapy., Methods: A total of 36 female patients with ALC and 36 with ABC, all of whom had completed their first cycle of chemotherapy, were included. Fatigue was assessed using the General Fatigue Scale (GFS), and sleep disturbances were evaluated using the Pittsburgh Sleep Quality Index (PSQI) at designated time points throughout the chemotherapy process., Results: Linear regression analysis indicated that variables such as age, education level, employment status, cancer type, clinical stage, and symptom distress had no significant correlation with either fatigue or sleep disturbances. The GFS significantly discriminated fatigue among the ALC, ABC, and combined groups, while the PSQI demonstrated a significant distinction in sleep disturbance only within the ALC and combined groups., Conclusions: In summary, when considering the findings of both assessments in this study, the GFS score exhibited greater sensitivity in detecting fatigue than the PSQI score did for identifying sleep disturbances in advanced cancer patients undergoing chemotherapy., (© 2023 The Author(s).)

This study aims to examine the effectiveness of chair yoga therapy on improving functional status and daily life activity scores in older female adults with knee osteoarthritis living in the community. A quasi-experimental design was adopted. In total, 85 female participants with knee osteoarthritis were assigned to the chair yoga therapy intervention group ( n = 43) or the comparison ( n = 42) group. A 12-week chair yoga exercise program was provided to the intervention group two times per week from January to April 2020. The primary outcomes, which include changes in physical functional ability, body mass index, and biophysiological indicators, were evaluated for all participants in the pre- and post-measures time periods. The analysis shows that the participants had a significantly higher level of functional fitness and daily life activity scores after the chair yoga intervention. This finding indicates that the chair yoga program was effective in improving the functional fitness and daily life activity scores of community-dwelling elderly females with knee osteoarthritis.

Background: Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited., Results: Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship., Conclusions: Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature., (© 2023. The Author(s).)

Home care patients have swallowing dysfunction and rely on an in-dwelling nasogastric tube (NGT) to complement oral food intake, supplement their diet, and maintain adequate nutritional status. This study explored the relationship between aspiration pneumonia (AP) and feeding care among home care patients with an in-dwelling NGT. This preliminary study employed a cross-sectional design. There were 35 patients who relied on an in-dwelling NGT to complement their oral intake of food (NGT-oral feeding) and their primary caregivers participated in this study. All of them developed AP in the past year. Factors involving food intake performance during mealtime of the home care patients and feeding care provided by the caregivers were simultaneously observed and recorded. Among the six risk factors univariately correlated with the incidence of AP, feeding in a noisy environment, using a large spoon to feed the participants, more than 5 mL of food per mouthful, food intake duration lasting > 30 min, swallowing twice for each mouthful of food, and coughing at least once every day remained significant in the logistic regression model (all p < 0.05). Four risk factors for AP were correlated with feeding care; the adjusted risk ratio ranged from 6.17 to 14.96 (all p < 0.05). In addition to each individual’s food intake ability, improper feeding assistance was related to the risk factors for AP among home care patients with NGT-oral feeding. Thus, home caregivers should receive safe oral feeding education and training.

Although the pan-genotypic direct-acting antiviral regimen was approved for treating chronic hepatitis C infection regardless of the hepatitis C virus (HCV) genotype, real-world data on its effectiveness against mixed-genotype or genotype-undetermined HCV infection are scarce. We evaluated the real-world safety and efficacy of two pan-genotypic regimens (Glecaprevir/Pibrentasvir and Sofosbuvir/Velpatasvir) for HCV-infected patients with mixed or undetermined HCV genotypes from the five hospitals in the Changhua Christian Care System that commenced treatment between August 2018 and December 2020. This retrospective study evaluated the efficacy and safety of pan-genotypic direct-acting antiviral (DAA) treatment in adults with HCV infection. The primary endpoint was the sustained virological response (SVR) observed 12 weeks after completing the treatment. Altogether, 2446 HCV-infected patients received the pan-genotypic DAA regimen, 37 (1.5%) patients had mixed-genotype HCV infections and 110 (4.5%) patients had undetermined HCV genotypes. The mean age was 63 years and 55.8% of our participants were males. Nine (6.1%) patients had end-stage renal disease and three (2%) had co-existing hepatomas. We lost one patient to follow-up during treatment and one more patient after treatment. A total of four patients died. However, none of these losses were due to treatment-related side effects. The rates of SVR12 for mixed-genotype and genotype-undetermined infections were 97.1% and 96.2%, respectively, by per-protocol analyses, and 91.9% and 92.7% respectively, by intention-to-treat population analyses. Laboratory adverse events with grades ≥3 included anemia (2.5%), thrombocytopenia (2.5%), and jaundice (0.7%). Pan-genotypic DAAs are effective and well-tolerated for mixed-genotype or genotype-undetermined HCV infection real-world settings.

The Bengalese finch was domesticated more than 250 years ago from the wild white-rumped munia (WRM). Similar to other domesticated species, Bengalese finches show a reduced fear response and have lower corticosterone levels, compared to WRMs. Bengalese finches and munias also have different song types. Since oxytocin (OT) has been found to be involved in stress coping and auditory processing, we tested whether the OT sequence and brain expression pattern and content differ in wild munias and domesticated Bengalese finches. We sequenced the OT from 10 wild munias and 11 Bengalese finches and identified intra-strain variability in both the untranslated and protein-coding regions of the sequence, with all the latter giving rise to synonymous mutations. Several of these changes fall in specific transcription factor-binding sites, and show either a conserved or a relaxed evolutionary trend in the avian lineage, and in vertebrates in general. Although in situ hybridization in several hypothalamic nuclei did not reveal significant differences in the number of cells expressing OT between the two strains, real-time quantitative PCR showed a significantly higher OT mRNA expression in the cerebrum of the Bengalese finches relative to munias, but a significantly lower expression in their diencephalon. Our study thus points to a brain region-specific pattern of neurochemical expression in domesticated and wild avian strains, which could be linked to domestication and the behavioral changes associated with it., (© 2021 The Authors. Genes, Brain and Behavior published by International Behavioural and Neural Genetics Society and John Wiley & Sons Ltd.)

Background: Glecaprevir/pibrentasvir is a protease inhibitor-containing pangenotypic direct-acting antiviral regimen that has been approved for the treatment of chronic hepatitis C. The present study aimed to evaluate the safety and efficacy of glecaprevir/pibrentasvir in patients with compensated cirrhosis in a real-world setting., Methods: We evaluated the real-world safety and efficacy of glecaprevir/pibrentasvir in patients with compensated cirrhosis from five hospitals in the Changhua Christian Care System, who underwent treatment between August 2018 and October 2020. The primary endpoint was a sustained virological response observed 12 weeks after completion of the treatment., Results: Ninety patients, including 70 patients who received the 12-week therapy and 20 patients who received the 8-week therapy, were enrolled. The mean age of the patients was 65 years, and 57.8% of the patients were males. Sixteen (17.8%) patients had end-stage renal disease, and 15 (16.7%) had co-existing hepatoma. The hepatitis C virus genotypes 1 (40%) and 2 (35.6%) were most common. The common side effects included anorexia (12.2%), pruritus (7.8%), abdominal discomfort (7.8%), and malaise (7.8%). Laboratory adverse grade ≥3 events included anemia (6.3%), thrombocytopenia (5.1%), and jaundice (2.2%). The overall sustained virological response rates were 94.4% and 97.7% in the intention-to-treat and per-protocol analyses, respectively., Conclusions: the glecaprevir/pibrentasvir treatment regimen was highly effective and well tolerated among patients with compensated cirrhosis in the real-world setting.

Personalized tongue pressure (TP) training focuses on improving swallowing. This study aims to establish the TP values of different age levels and compare changes between different swallowing status among community-dwelling elders. In this cross-sectional study, 1000 participants, aged 60 years old and above, were recruited from community care centers. All participants were classified into non chewing and/or swallowing difficulties (NCSD) and with chewing and/or swallowing difficulties (CSD) groups and their diseases and dieting status were recorded using a structured questionnaire. A disposable oral probe was used to measure TP by asking participants to compress it against the hard palate with maximum voluntary effort. Among 1000 elders, 63.10% had CSD and their TP (from 31.76 to 18.20 kPa) was lower than the NCSD group (from 33.56 to 24.51 kPa). Both groups showed the same tendency for TP decline with increasing age. Decline of TP makes CSD elderly have a poor appetite, eat a soft or liquid diet, and take longer to eat a meal (all p < 0.050). The secondary risk factor dominating TP decline for NCSD and CSD elders is having an education level less than primary school and an abnormal eating assessment, respectively. Our results demonstrated that TP decline has a significant relationship with age changes. Education level and an abnormal eating assessment score are closely associated with TP decline. A series of TP values can be used as a reference indicator of personalized medicine during the aging process among community-dwelling older adults.

An oral hygiene board game was designed as an intervention tool and applied to explore the effectiveness for the oral health related knowledge (OHK) score and plaque index (PI) of adults with intellectual disability (ID). This one-group pre/post-test design study was conducted in a residential long-term care facility for 42 participants. The study had one pre-test (baseline) and three post-tests evaluated in both control and intervention stages, respectively. The participants participated in a 60-min oral hygiene board game twice a week during the intervention stage. Total OHK score and PI of the participants were recorded to determine the effectiveness of intervention. There were no differences in OHK score and PI between the two stages at baseline. The results in intervention stage demonstrated a significant gradual increase and reduction in the OHK score when compared with the control stage. A statistically significant improvement in the OHK score and PI (42.29% and -33.28%, respectively) at the end of intervention between two stages was recorded. This study proved a board game is deemed an effective education method applicable to promote the OHK and skills of ID adults.

The evolution of flight in feathered dinosaurs and early birds over millions of years required flight feathers whose architecture features hierarchical branches. While barb-based feather forms were investigated, feather shafts and vanes are understudied. Here, we take a multi-disciplinary approach to study their molecular control and bio-architectural organizations. In rachidial ridges, epidermal progenitors generate cortex and medullary keratinocytes, guided by Bmp and transforming growth factor β (TGF-β) signaling that convert rachides into adaptable bilayer composite beams. In barb ridges, epidermal progenitors generate cylindrical, plate-, or hooklet-shaped barbule cells that form fluffy branches or pennaceous vanes, mediated by asymmetric cell junction and keratin expression. Transcriptome analyses and functional studies show anterior-posterior Wnt2b signaling within the dermal papilla controls barbule cell fates with spatiotemporal collinearity. Quantitative bio-physical analyses of feathers from birds with different flight characteristics and feathers in Burmese amber reveal how multi-dimensional functionality can be achieved and may inspire future composite material designs. VIDEO ABSTRACT., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler ( Cyanoderma ruficeps Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter. Nevertheless, assembly completeness showed little difference among the trimming strategies. One should determine the optimal trimming strategy based on what the assembled genome will be used for. For example, to identify single nucleotide polymorphisms (SNPs) associated with phenotypic evolution, applying PLATANUS to gently trim reads would yield a reference genome with a slightly shorter scaffold length (N50 = 15.64 vs. 16.89 Mb) than the raw reads, but would save 75% of computational time. We also found that chromosomes Z, W, and 4A of the rufous-capped babbler were poorly assembled, likely due to a recently fused, neo-sex chromosome. The rufous-capped babbler genome with long scaffolds and quality gene annotation can provide a good system to study avian ecological adaptation in East Asia.

Genetic isolation of populations over evolutionary time leads to the formation of independent species. We examined a pair of shorebirds - the Kentish Plover Charadrius alexandrinus and the enigmatic White-faced Plover C. dealbatus - which display strong plumage differentiation, yet show minimal genetic divergence based on previous mitochondrial and microsatellite work. Two scenarios may lead to this situation: (1) they represent clinal or poorly diverged populations with limited genomic differentiation despite substantial plumage variation, or (2) they are diverging taxa at the cusp of speciation, with ongoing limited gene flow obliterating signals of differentiation in traditional genetic markers. We compared the genotypes of 98 plovers (59 Kentish Plovers, 35 White-faced Plovers and 4 genomic hybrids) sampled in eastern Asia and Europe using ddRADSeq to harvest over 8000 genome-wide SNPs. In contrast to previous studies, our analyses revealed two well defined genomic clusters, with limited hybridization and a narrow contact zone. We also uncovered significant differences in bill length and further sex-specific differences in size, which may signal differences in mate choice between Kentish and White-faced Plovers. Our results support the hypothesis that this shorebird duo is on the verge of speciation.

What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill ( Sinosuthora webbiana ) in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation. Parrotbills at both high and low altitudes exhibited signatures of recent selection, suggesting that not only the front but also the trailing edges of postglacial expanding populations could be subjected to environmental stresses. This study verifies and quantifies the importance of standing variation in adaptation in a cohort of genes, illustrating that the evolutionary potential of a population depends significantly on its preexisting genetic diversity. These findings provide important context for understanding adaptation and conservation of species in the Anthropocene., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Background: A variety of human diseases transmitted by arthropod vectors, including ticks, are emerging around the globe. Birds are known to be hosts of ticks and can disperse exotic ticks and tick-borne pathogens. In Taiwan, previous studies have focused predominantly on mammals, leaving the role of birds in the maintenance of ticks and dissemination of tick-borne pathogens undetermined., Methods: Ticks were collected opportunistically when birds were studied from 1995 to 2013. Furthermore, to improve knowledge on the prevalence and mean load of tick infestation on birds in Taiwan, ticks were thoroughly searched for when birds were mist-netted at seven sites between September 2014 and April 2016 in eastern Taiwan. Ticks were identified based on both morphological and molecular information and were screened for potential tick-borne pathogens, including the genera Anaplasma, Babesia, Borrelia, Ehrlichia and Rickettsia. Finally, a list of hard tick species collected from birds in Taiwan was compiled based on past work and the current study., Results: Nineteen ticks (all larvae) were recovered from four of the 3096 unique mist-netted bird individuals, yielding a mean load of 0.006 ticks/individual and an overall prevalence of 0.13%. A total of 139 ticks from birds, comprising 48 larvae, 35 nymphs, 55 adults and one individual of unknown life stage, were collected from 1995 to 2016, and 11 species of four genera were identified, including three newly recorded species (Haemaphysalis wellingtoni, Ixodes columnae and Ixodes turdus). A total of eight tick-borne pathogens were detected, with five species (Borrelia turdi, Anaplasma sp. clone BJ01, Ehrlichia sp. BL157-9, Rickettsia helvetica and Rickettsia monacensis) not previously isolated in Taiwan. Overall, 16 tick species of five genera have been recorded feeding on birds, including nine species first discovered in this study., Conclusion: Our study demonstrates the paucity of information on ticks of birds and emphasizes the need for more research on ticks of birds in Taiwan and Southeast Asia. Moreover, some newly recorded ticks and tick-borne pathogens were found only on migratory birds, demonstrating the necessity of further surveillance on these highly mobile species.

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations.

Sexual dichromatism is a key proxy for the intensity of sexual selection. Studies of dichromatism in birds may, however, have underestimated the intensity and complexity of sexual selection because they used museum specimens alone without taking colour-fading into account or only measured conspicuous visual traits in live animals. We investigated whether the Himalayan black bulbul (Hypsipetes leucocephalus nigerrimus), which is sexually monomorphic to the human eye, exhibits sexual dichromatism distinguishable by a spectrometer. We measured the reflectance (within both the human visual perceptive and the ultraviolet ranges) of two carotenoid-based parts and eight dull and melanin-based parts for each individual live bird or museum skin sampled. According to an avian model of colour discrimination thresholds, we found that males exhibited perceptibly redder beaks, brighter tarsi and darker plumage than did females. This suggests the existence of multiple cryptic sexually dichromatic traits within this species. Moreover, we also observed detectable colour fading in the museum skin specimens compared with the live birds, indicating that sexual dichromatism could be underestimated if analysed using skin specimens alone.

Background: Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction., Objective: Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples., Methods: We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues., Results: Ten genes ( ABCG2 , AQP8 , SPIB, CA7 , CLDN8 , SCNN1B , SLC30A10 , CD177 , PADI2 , and TGFBI ) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method., Conclusions: Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis., Competing Interests: The authors declare there are no competing interests.

Aim: To verify gene expression profiles for colorectal cancer using 12 internet public microarray datasets., Methods: Logistic regression analysis was performed, and odds ratios for each gene were determined between colorectal cancer (CRC) and controls. Twelve public microarray datasets of GSE 4107, 4183, 8671, 9348, 10961, 13067, 13294, 13471, 14333, 15960, 17538, and 18105, which included 519 cases of adenocarcinoma and 88 normal mucosa controls, were pooled and used to verify 17 selective genes from 3 published studies and estimate the external generality., Results: We validated the 17 CRC-associated genes from studies by Chang et al (Model 1: 5 genes), Marshall et al (Model 2: 7 genes) and Han et al (Model 3: 5 genes) and performed the multivariate logistic regression analysis using the pooled 12 public microarray datasets as well as the external validation. The goodness-of-fit test of Hosmer-Lemeshow (H-L) showed statistical significance (P = 0.044) for Model 2 of Marshall et al in which observed event rates did not match expected event rates in subgroups of the model population. Expected and observed event rates in subgroups were similar, which are called well calibrated, in Models 1, 3 and 4 with non-significant P values of 0.460, 0.194 and 1.000 for H-L tests, respectively. A 7-gene model of CPEB4, EIF2S3, MGC20553, MS4A1, ANXA3, TNFAIP6 and IL2RB was pairwise selected, which showed the best results in logistic regression analysis (H-L P = 1.000, R (2) = 0.951, areas under the curve = 0.999, accuracy = 0.968, specificity = 0.966 and sensitivity = 0.994)., Conclusion: A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.

Aim: Optimal molecular markers for detecting colorectal cancer (CRC) in a blood-based assay were evaluated., Methods: A matched (by variables of age and sex) case-control design (111 CRC and 227 non-cancer samples) was applied. Total RNAs isolated from the 338 blood samples were reverse-transcribed, and the relative transcript levels of candidate genes were analyzed. The training set was made of 162 random samples of the total 338 samples. A logistic regression analysis was performed, and odds ratios for each gene were determined between CRC and non-cancer. The samples (n = 176) in the testing set were used to validate the logistic model, and an inferred performance (generality) was verified. By pooling 12 public microarray datasets(GSE 4107, 4183, 8671, 9348, 10961, 13067, 13294, 13471, 14333, 15960, 17538, and 18105), which included 519 cases of adenocarcinoma and 88 controls of normal mucosa, we were able to verify the selected genes from logistic models and estimate their external generality., Results: The logistic regression analysis resulted in the selection of five significant genes (P < 0.05; MDM2, DUSP6, CPEB4, MMD, and EIF2S3), with odds ratios of 2.978, 6.029, 3.776, 0.538 and 0.138, respectively. The five-gene model performed stably for the discrimination of CRC cases from controls in the training set, with accuracies ranging from 73.9% to 87.0%, a sensitivity of 95% and a specificity of 95%. In addition, a good performance in the test set was obtained using the discrimination model, providing 83.5% accuracy, 66.0% sensitivity, 92.0% specificity, a positive predictive value of 89.2% and a negative predictive value of 73.0%. Multivariate logistic regressions analyzed 12 pooled public microarray data sets as an external validation. Models that provided similar expected and observed event rates in subgroups were termed well calibrated. A model in which MDM2, DUSP6, CPEB4, MMD, and EIF2S3 were selected showed the result in logistic regression analysis (H-L P = 0.460, R2= 0.853, AUC = 0.978, accuracy = 0.949, specificity = 0.818 and sensitivity = 0.971)., Conclusion: A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.

Background: Microarray technology shows great potential but previous studies were limited by small number of samples in the colorectal cancer (CRC) research. The aims of this study are to investigate gene expression profile of CRCs by pooling cDNA microarrays using PAM, ANN, and decision trees (CART and C5.0)., Methods: Pooled 16 datasets contained 88 normal mucosal tissues and 1186 CRCs. PAM was performed to identify significant expressed genes in CRCs and models of PAM, ANN, CART, and C5.0 were constructed for screening candidate genes via ranking gene order of significances., Results: The first screening identified 55 genes. The test accuracy of each model was over 0.97 averagely. Less than eight genes achieve excellent classification accuracy. Combining the results of four models, we found the top eight differential genes in CRCs; suppressor genes, CA7, SPIB, GUCA2B, AQP8, IL6R and CWH43; oncogenes, SPP1 and TCN1. Genes of higher significances showed lower variation in rank ordering by different methods., Conclusion: We adopted a two-tier genetic screen, which not only reduced the number of candidate genes but also yielded good accuracy (nearly 100%). This method can be applied to future studies. Among the top eight genes, CA7, TCN1, and CWH43 have not been reported to be related to CRC.

When geographic isolation drives speciation, concurrent termination of gene flow among genomic regions will occur immediately after the formation of the barrier between diverging populations. Alternatively, if speciation is driven by ecologically divergent selection, gene flow of selectively neutral genomic regions may go on between diverging populations until the completion of reproductive isolation. It may also lead to an unsynchronized termination of gene flow between genomic regions with different roles in the speciation process. Here, we developed a novel Approximate Bayesian Computation pipeline to infer the geographic mode of speciation by testing for a lack of postdivergence gene flow and a concurrent termination of gene flow in autosomal and sex-linked markers jointly. We applied this approach to infer the geographic mode of speciation for two allopatric highland rosefinches, the vinaceous rosefinch Carpodacus vinaceus and the Taiwan rosefinch C. formosanus from DNA polymorphisms of both autosomal and Z-linked loci. Our results suggest that the two rosefinch species diverged allopatrically approximately 0.5 Ma. Our approach allowed us further to infer that female effective population sizes are about five times larger than those of males, an estimate potentially useful when comparing the intensity of sexual selection across species.

Background: Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic regression (LR) and two composite models of DT-ANN and DT-LR. The collection of microarray datasets from the Gene Expression Omnibus, four breast cancer datasets were pooled for predicting five-year breast cancer relapse. After data compilation, 757 subjects, 5 clinical variables and 13,452 genetic variables were aggregated. The bootstrap method, Mann-Whitney U test and 20-fold cross-validation were performed to investigate candidate genes with 100 most-significant p-values. The predictive powers of DT, LR and ANN models were assessed using accuracy and the area under ROC curve. The associated genes were evaluated using Cox regression., Results: The DT models exhibited the lowest predictive power and the poorest extrapolation when applied to the test samples. The ANN models displayed the best predictive power and showed the best extrapolation. The 21 most-associated genes, as determined by integration of each model, were analyzed using Cox regression with a 3.53-fold (95% CI: 2.24-5.58) increased risk of breast cancer five-year recurrence., Conclusions: The 21 selected genes can predict breast cancer recurrence. Among these genes, CCNB1, PLK1 and TOP2A are in the cell cycle G2/M DNA damage checkpoint pathway. Oncologists can offer the genetic information for patients when understanding the gene expression profiles on breast cancer recurrence.

The genes encoding the enzymes for metabolising alcohol dehydrogenase 1B (ADH1B) and aldehyde dehydrogenase 2 (ALDH2) - exhibit genetic polymorphism and ethnic variations. Although the ALDH2*2 variant allele has been widely accepted as protecting against the development of alcoholism in Asians, the association of the ADH1B*2 variant allele with drinking behaviour remains inconclusive. The goal of this study was to determine whether the polymorphic ADH1B and ALDH2 genes are associated with stroke in male Han Chinese with high alcohol consumption. Sixty-five stroke patients with a history of heavy drinking (HDS) and 83 stroke patients without such a history (NHDS) were recruited for analysis of the ADH1B and ALDH2 genotypes from the stroke registry in the Tri-Service General Hospital, Taipei, Taiwan, between January 2000 and December 2001. The allelotypes of ADH1B and ALDH2 were determined using the polymerase chain reaction-restriction fragment length polymorphism method. The HDS patients (3 per cent) showed a significantly lower ALDH2*2 allele frequency than NHDS patients (27 per cent) (p < 0.001). After controlling for age, patients with HDS were associated with a significantly higher occurrence of cigarette smoking (p < 0.01) and liver dysfunction (p < 0.01). Multiple logistic regression analyses revealed that the ALDH2*2 variant allele was an independent variable exhibiting strong protection (odds ratio 0.072; 95 per cent confidence interval 0.02-0.26) against HDS after adjustment for hypertension, diabetes mellitus, smoking status and liver dysfunction. By contrast, allelic variations in ADH1B exerted no significant effect on HDS. The present study indicated that, unlike ALDH2*2, ADH1B*2 appears not to be a significant negative risk factor for high alcohol consumption in male Han Chinese with stroke.

Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10(-8)) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we discuss the potential importance of evolutionarily labile traits with significant fitness consequences, such as migratory behavior and habitat preference, in facilitating divergence of the spoonbills.

Background: The subtropical island of Taiwan is an area of high endemism and a complex topographic environment. Phylogeographic studies indicate that vicariance caused by Taiwan's mountains has subdivided many taxa into genetic phylogroups. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the evolutionary history of an endemic montane bird, Steere's Liocichla (Liocichla steerii), fit the general vicariant paradigm for a montane organism., Results: We found that while mountains appear to channel gene flow they are not a significant barrier for Steere's Liocichla. Recent demographic expansion was evident, and genetic diversity was relatively high across the island, suggesting expansion from multiple areas rather than a few isolated refugia. Ecological niche modeling corroborated the molecular results and suggested that populations of Steere's Liocichla are connected by climatically suitable habitat and that there was less suitable habitat during the Last Glacial Maximum., Conclusions: Genetic and ecological niche modeling data corroborate a single history--Steere's Liocichla was at lower density during the Last Glacial Maximum and has subsequently expanded in population density. We suggest that such a range-wide density expansion might be an overlooked cause for the genetic patterns of demographic expansion that are regularly reported. We find significant differences among some populations in FST indices and an admixture analysis. Though both of these results are often used to suggest conservation action, we affirm that statistically significant results are not necessarily biologically meaningful and we urge caution when interpreting highly polymorphic data such as microsatellites.

Background: Combination of CHD (chromo-helicase-DNA binding protein)-specific polymerase chain reaction (PCR) with electrophoresis (PCR/electrophoresis) is the most common avian molecular sexing technique but it is lab-intensive and gel-required. Gender determination often fails when the difference in length between the PCR products of CHD-Z and CHD-W genes is too short to be resolved., Results: Here, we are the first to introduce a PCR-melting curve analysis (PCR/MCA) to identify the gender of birds by genomic DNA, which is gel-free, quick, and inexpensive. Spilornis cheela hoya (S. c. hoya) and Pycnonotus sinensis (P. sinensis) were used to illustrate this novel molecular sexing technique. The difference in the length of CHD genes in S. c. hoya and P. sinensis is 13-, and 52-bp, respectively. Using Griffiths' P2/P8 primers, molecular sexing failed both in PCR/electrophoresis of S. c. hoya and in PCR/MCA of S. c. hoya and P. sinensis. In contrast, we redesigned sex-specific primers to yield 185- and 112-bp PCR products for the CHD-Z and CHD-W genes of S. c. hoya, respectively, using PCR/MCA. Using this specific primer set, at least 13 samples of S. c. hoya were examined simultaneously and the Tm peaks of CHD-Z and CHD-W PCR products were distinguished., Conclusion: In this study, we introduced a high-throughput avian molecular sexing technique and successfully applied it to two species. This new method holds a great potential for use in high throughput sexing of other avian species, as well.