bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Pickles: Biological and Sociocultural Links Between Fermented Foods and the Human Gut Microbiome
Authors: Flachs Andrew , Orkin Joseph 
Published: March 2021

Abstract
BackgroundThe composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa. MethodsIn this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews and participated in a four-day craft fermentation workshop, and then collected both fermented food products and stool samples from workshop participants eating those fermented foods. ResultsWe identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 ASVs shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes. ConclusionsBy combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally-informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.
Exploring the impact of complex diseases on non-diseased human tissue transcriptomes
Authors: Poon Chi-Lam , Chen Cho-Yi 
Published: March 2021

Abstract
Background

The development of complex diseases is contributed by the combination of multiple factors and complicated interactions between them. Inflammation has recently been associated with many complex diseases and may cause long-term damage to the human body. In this study, we examined whether two types of complex disease systematically altered the transcriptomes of non-diseased human tissues and whether inflammation was linked to identifiable molecular signatures, using post-mortem samples from the Genotype-Tissue Expression (GTEx) project.
Results

Following a series of differential expression (DE) analyses, dozens to hundreds of DE genes were identified in multiple tissues between subjects with and without a history of cerebrovascular disease (CVD) or major depression (MD). DE genes from these disease-associated tissues—the visceral adipose, tibial artery, caudate, and spinal cord for CVD; and the hypothalamus, putamen, and spinal cord for MD—were further analyzed for functional enrichment. Many pathways associated with immunological events were positively enriched in the DEGs of the CVD-associated tissues, as were the neurological and metabolic pathways in the MD-associated tissues. Eight gene–tissue pairs were found to overlap with those prioritized by our transcriptome-wide association studies (TWAS), indicating a potential genetic effect on gene expression for circulating cytokine phenotypes.
Conclusions

Complex diseases like CVD and MD may cause observable changes in the gene expression of non-diseased tissues, suggesting that a long-term impact of diseases, lifestyles and environmental factors may together contribute to the appearance of transcriptomic “scars” on the human body. Furthermore, inflammation is probably one of the systemic and long-lasting effects of cerebrovascular events.
Corilagin Reduces Resistance to PARP Inhibitors by Inhibiting the ERK Signaling Pathway in Ovarian Cancers
Authors: Luan Baoxin , Zhao Hongbo , Bast Robert C. , Lu Zhen , Yu Yinhua 
Published: March 2021

Abstract
Background: Corilagin is a compound with hepatoprotective and antiviral activity extracted from Phyllanthus niruri L. Our previous work demonstrated that corilagin inhibits the growth of ovarian cancer cells by regulating the TGF-β/AKT/ERK signaling. Corilagin was also found to sensitize ovarian cancer cells to paclitaxel and carboplatin by inhibiting the Snail-glycolysis pathway. We have now studied whether corilagin could overcome resistance of ovarian cancer cells to poly ADP ribose polymerase inhibitors (PARPi). PARPi block DNA base excision repair and have been approved for treatment of ovarian cancers. Drug resistance has limited efficacy of PARPi. Methods: We have assessed the effect of corilagin alone and in combination with PARPi in two pairs of ovarian cancer cell lines-A2780CP/A2780CP_R and UWB1.289/UWB1.289_R-that are sensitive or resistant to PARPi. CulcuSyn software (BIOSOFT-Software for Science, Cambridge, U.K.) was used to calculate synergy between two drug combinations. Results: Corilagin was active against all four cell lines and enhanced BMN673 activity synergistically in both PARPi resistant cell lines. PARPi-BMN673 down-regulated the expression levels of PARP and up-regulated pH2AX, it decreased pERK activity in sensitive cell lines, but not in resistant cell lines. While corilagin affected DNA repair function to some extent, it inhibited pERK activity in both PARPi sensitive and resistant cells in a dose dependent manner. Corilagin, but not the BMN673, inhibited ZEB1 in resistant cells. Conclusions: Corilagin deserves further evaluation as a drug that could enhance the activity of PARPi in PARPi-resistant ovarian cancer cells.
Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs
Authors: Nosková Adéla , Bhati Meenu , Kadri Naveen Kumar , Crysnanto Danang , Neuenschwander Stefan , Hofer Andreas , Pausch Hubert 
Published: March 2021

Abstract
Background
The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.
Results
Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping.
Conclusions
We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.
Rural-urban Correlates of Modern Contraceptives Utilization Among Adolescents in Zambia: a National Cross-sectional Survey
Authors: Sserwanja Quraish , Musaba Milton W. , Mutisya Linet M. , Mukunya David 
Published: March 2021

Abstract
Background: Modern contraceptive use among adolescents is low despite the adverse effects of adolescent pregnancies and births. Understanding the predictors of modern contraceptive use in different settings is key to design effective context-specific interventions. We aimed to determine factors associated with modern contraceptives use among adolescents in rural and urban settings of Zambia. Methods: We analyzed data from 2018 Zambia demographic and health survey (ZDHS) focusing on adolescent girls aged 15–19 years. We conducted multilevel logistic regression using SPSS version 25 to examine rural-urban variations in factors associated with modern contraceptive utilization.Results: Overall, 12.0% (360/3000, 95% CI: 10.9-13.2) of adolescents in Zambia were using modern contraceptives. Use of modern contraceptives was higher in rural areas at 13.7% (230/1677, 95% CI: 12.1-15.3) compared to 9.8% (130/1323, 95% CI: 8.3-11.6) in urban areas. In the rural areas, having a child (aOR = 13.46; 95% CI 8.28 to 21.90), marriage (aOR = 1.97; 95% CI 1.25 to 3.08), older age (being 19 years) (aOR = 3.97; 95% CI 1.51 to 10.1) and belonging to the richest wealth quintile (aOR = 3.01; 95% CI 1.06 to 8.58) were positively associated with contraceptive utilization. In the urban areas, older age (being 19 years) (aOR = 4.80; 95% CI 1.55 to 14.84) and having a child (aOR = 18.52; 95% CI 9.50 to 36.14) were the only factors positively associated with modern contraceptive utilization.Conclusions: Having shown that some factors (age and having a child) were associated with modern contraceptive use in both rural and urban areas while some were only significant in rural areas (province, marital status and wealth index), indicates that the urban-rural differences in modern contraceptives use are both due to differences in the levels and nature or type of determinants. Therefore, interventions aiming to increase contraceptive utilization should be context specific.
Hemoglobin A1c and Vaginitis: National Health and Nutrition Examination Survey 2001-2004 Experience
Authors: Stennett Christina A. , Turpin Rodman , Robbins Sarah J. , Brotman Rebecca M. , Miller Ryan S. 
Published: March 2021

Abstract
Objectives: It is well-documented that diabetes mellitus is associated with increased risk for vulvovaginal candidiasis. We sought to assess whether diabetes (assessed by HbA1c) might be similarly associated with other vaginitis outcomes (bacterial vaginosis (BV) and Trichomonas vaginalis (TV)) infection). We hypothesized that glucose may favor the growth of BV-associated bacteria, and high blood glucose may also affect host immune responses, potentially increasing risk for BV and TV infection. Our secondary data analysis utilized a large population-based study, the 2001-2004 U.S. National Health and Nutrition Examination Survey (NHANES). Results: Among 2,442 reproductive-age women with available data, 54 (unweighted) had elevated HbA1c (>6.4) indicating diabetes, 112 had borderline HbA1c (5.7–6.4), 791 had BV by Nugent’s Gram stain score (Nugent-BV), and 104 had TV. Borderline HbA1c, but not higher HbA1c, was significantly associated with Nugent-BV (OR=1.58, 95% CI: 1.11-2.25) and TV detection (OR=2.45, 95% CI: 1.10-5.44) in unadjusted logistic regression models. After adjustment for confounders, including race/ethnicity, recent douching, and body mass index, associations between borderline HbA1c and both vaginitis outcomes were null. Sample size was limited by few cases with diabetes, and multivariable modeling may require larger sample size. Future longitudinal studies with more diabetes cases may confirm these findings.
Three-month early change in prostate-specific antigen levels as a predictive marker for overall survival during hormonal therapy for metastatic hormone-sensitive prostate cancer
Authors: Nakanishi Shotaro , Goya Masato , Tamaki Mitsuyoshi , Oshiro Takuma , Saito Seiichi 
Published: March 2021

Abstract
Objective: To date, there are no useful markers for predicting the prognosis of metastatic hormone-sensitive prostate cancer (mHSPC). We evaluated the effect of early changes in prostate-specific antigen (PSA) levels after androgen deprivation therapy (ADT) on castration-resistant prostate cancer (CRPC) progression and overall survival (OS) in mHSPC patients. Results: In 71 primary mHSPC patients treated with ADT, the median times to CRPC and OS were 15 months and 92 months, respectively. In multivariate analysis, a Gleason score of ≥8 (p = 0.004), an extent of disease value (EOD) of ≥2 (p = 0.004), and a 3-month PSA level >1% of the pretreatment level (p = 0.017) were independent predictors of shorter time to CRPC. The area under the receiver operating characteristic curve was feasible at 0.822. For OS, a 3-month PSA level >1% of the pretreatment level was an independent predictor of time to CRPC (p = 0.004).Three factors were independent predictors of shorter time to CRPC. A 3-month PSA level >1% of the pretreatment level correlated with poor a prognosis.
Analysis of the effect of fingertip size for sex differences in current perception thresholds with transcutaneous electrical stimulation in healthy subjects
Authors: Seno Shin-ichiro , Shimazu Hideaki , Kogure Eiki , Watanabe Atsushi , Kobayashi Hiroko 
Published: March 2021

Abstract
Objective

This study aimed to measure the current perception threshold (CPT) of five fingertips of the left hand in healthy subjects and analyze whether sex differences in perception thresholds are suppressed when adjusting for fingertip size among males and females.
Results

For fingertips from the thumb to the little finger, the males’ CPT values were 1.03, 0.83, 0.86, 0.86, and 0.88 mA; the females’ results were 0.63, 0.55, 0.54, 0.51, and 0.50 mA. The CPTs were higher in males than in females for every fingertip. Upon adjusting for fingertip length, the log-transformed CPT values were found to have sex differences, except for the index finger: thumb, t(20.05) = 3.493, p = 0.002; middle finger, U(30) = 44.50, p = 0.005; ring finger, t(30) = 55.50, p = 0.018; little finger, U(30) = 30.00, p = 0.001. Similarly, the CPT values, transformed into log values when adjusting for the fingertip area, were found to have sex differences for three fingertips: thumb, t(18) = 2.649, p = 0.016; middle finger, U(20) = 12.00, p = 0.004; ring finger, t(18) = 2.206, p = 0.041. According to this study, sex differences in CPTs were not completely abolished by adjusting for fingertip length or area.
Functional-Specific Projections from V2 to V4 in Macaque Monkeys
Authors: Fang Chen , Yan Kun , Liang Chen , Wang Jiayu , Cai Xingya , Zhang Rui , Lu Haidong D. 
Published: March 2021

Abstract
Previous studies have revealed modular projections from area V2 to area V4 in macaques. Specifically, V2 neurons in cytochrome oxidase (CO)-rich thin and CO-sparse pale stripes project to distinct regions in V4. However, how these modular projections relate to the functional subcompartments of V4 remains unclear. In this study, we injected retrograde fluorescent tracers into different functional domains (color, orientation, and direction) in V4 that were identified with intrinsic signal optical imaging. We examined the labeled neurons in area V2 and their locations with respect to the CO patterns. Covariation was observed between the functional properties of the V4 injection sites and the numbers of labeled neurons in particular CO stripes. This covariation indicates that the color domains in V4 mainly received inputs from V2 thin stripes, whereas V4 orientation domains received inputs from pale (major) and thick (minor) stripes. Although there are motion-sensitive domains in both V2 and V4, our results did not reveal a functional-specific feedforward projection between them. These results confirmed previous findings of modular projections from V2 to V4 and provided functional specificity for these anatomical projections. Together, these findings indicate that color and form remain separate in the ventral midlevel visual processing.
Root Foraging Precision: Do Experimental Conditions Matter?
Authors: Stiblíková Pavlína , Weiser Martin 
Published: March 2021

Abstract
Purpose: Root foraging precision, i.e., preferential root proliferation in nutrient-rich patches in heterogeneous soil, contributes significantly to plant nutrient acquisition. The ability to forage is usually studied experimentally, although often under different conditions. It remains unclear whether different experimental conditions affect root foraging precision. We studied the effect of experiment duration, pot size and root separation on root foraging precision and the appropriateness of using root foraging as species-specific values in databases and meta-analyses.Methods: We cultivated three perennial species in pots with spatially heterogeneous nutrient supplies and manipulated the experiment duration (4 – 10 weeks). We partly replicated the experiment in two consecutive years. In two of the three species we compared outcomes when root types were separated and unseparated, and for one species we also manipulated pot size. We assessed the effects of the manipulated factors on foraging precision expressed as the ratio of root biomass in nutrient-rich and poor patches.Results: Root foraging precision was not affected by experiment duration or pot size. Separating roots to use only the fine ones for root foraging assessment amplified foraging precision values and reduced their intraspecific variation.Conclusions: Our study investigated various methods of the root foraging research and their impact on the root foraging precision. Root foraging precision is invariable to the studied factors, therefore it is suitable as a species-specific trait, if the effect of other factors (such as nutrient patch characteristics) is taken into account.
Recognize the role of CD146/MCAM in the osteosarcoma progression
Authors: Lei Xing , Wang Kewei , Wang Wenbo , Jin Hao , Gu Wenguang , Chen Zhiguo , Wang Wei , Gao Kaituo , Wang Huan 
Published: March 2021

Abstract
Background: Osteosarcoma (OS) is a common malignant bone tumor with poor prognosis. We previously reviewed that CD146 is correlated with multiple cancer progression, while its impact on OS is currently not systematically studied. Methods: we transfected MG63 with lentivirus to express CD146 ectopically, combining with anti-CD146 neutralizing antibody ab75769 to inhibit 143B, to observe the intrinsic relationship between CD146 and OS. In addition, we used Transwell co-culture system and self-designed cyclic migration assay to explore the effect of CD146 on the interaction between OS and endothelium. Finally, we also detected the expression of CD146 in OS under different culture conditions, including hyperoxia, low oxygen, high glucose and low glucose conditions.Results: CD146 promoted the colony formation, migration, invasion and homotypic adhesion of OS cells, and reducing the concentration of soluble CD146 in the OS medium inhibited the proliferation, migration and lumen formation of the cultured endothelium. However, CD146 did not affect the adhesion between OS and endothelium, nor did co-culture of both sides affect the CD146 expression. Similarly, the proliferation, migration and CD146 expression of MG63 remained unchanged after many cycles of migration itself, as did its co-culture with 143B for expressing CD146. In addition, we also showed that high glucose promoted the expression of CD146 in OS, while hypoxia had the opposite effect. Conclusions: These ﬁndings demonstrate that CD146 promotes OS progression by mediating pro-tumoral and angiogenic effects. Thus, CD146 could be a potential therapeutic target for OS, especially for OS patients with diabetes.
A Special Treatment of Vulvar Cancer with Pelvic Organ Prolapse: A Case Report
Authors: tang qin , wang ping 
Published: March 2021

Abstract
Background: Pelvic organ prolapse is a common benign condition in women, defined as the descent of one or more of the following: anterior vaginal wall; posterior vaginal wall; uterus (cervix); and apex of the vagina (vaginal vault or cuff scar after hysterectomy). Vulvar cancer is uncommon, accounting for 2-5% of gynecologic malignancies. Vulvar cancer and pelvic organ prolapse tend to occur in elderly individuals with other complications, such as heart disease, hypertension and diabetes. Risk during the perioperative period is very high; therefore, gynecologists should provide the most appropriate and comprehensive treatment plan to achieve a good prognosis. Case presentation: The patient’s main concerns is vulva pruritus and vulva mass prolapse. Important clinical examinations include vulvar biopsy suggesting vulvar carcinoma, and the POP Quantification (POP-Q) scores showing Aa:+2, Ba:+2, C:0, D:0, Ap:+1, Bp:+1. The primary diagnoses is highly differentiated squamous cell carcinoma of the vulva, pelvic organ prolapse. The patient underwent extensive vulvotomy, vulvoplasty, partial urethrotomy, external urethroplasty, partial cervicectomy, anterior and posterior vaginal wall repair, sacrospinous ligament suspension, and laparoscopic bilateral inguinal lymph node dissection. The patient recovered well and was discharged from hospital. But unfortunately, the patient was followed-up via telephone and died 1 year after surgery. Conclusions: Vulvar cancer and pelvic organ prolapse tend to occur in elderly individuals with other complications, such as heart disease, hypertension and diabetes. Risk during the perioperative period is very high; therefore, gynecologists should provide the most appropriate and comprehensive treatment plan to achieve a good prognosis.