bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping
Authors: Grohmann Caleb J. , Shull Caleb M. , Crum Tamar E. , Schwab Clint , Safranski Timothy J. , Decker Jared E. 
Published: September 2023

Abstract
Background
Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied generation proxy selection mapping (GPSM), a genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes (38,294–46,458 markers) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8447 pigs per population) to identify loci responding to artificial selection over a period of five to ten years. Gene-drop simulation analyses were conducted to provide context for the GPSM results. Selected loci within and across each population of pigs were compared in the context of swine breeding objectives.

Results
The GPSM identified 49 to 854 loci as under selection (Q-values less than 0.10) across 15 subsets of pigs based on combinations of populations. The number of significant associations increased when data were pooled across populations. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across these pig populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were found when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations.

Conclusions
This work confirms the efficacy and the negligible error rates of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. The identified polygenic selection highlights loci that are important to swine production.
Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets
Authors: Domingo Juan , Leon Teresa , Dura Esther 
Published: September 2023

Abstract
Background
Partitioning around medoids (PAM) is one of the most widely used and successful clustering method in many fields. One of its key advantages is that it only requires a distance or a dissimilarity between the individuals, and the fact that cluster centers are actual points in the data set means they can be taken as reliable representatives of their classes. However, its wider application is hampered by the large amount of memory needed to store the distance matrix (quadratic on the number of individuals) and also by the high computational cost of computing such distance matrix and, less importantly, by the cost of the clustering algorithm itself.

Results
Therefore, new software has been provided that addresses these issues. This software, provided under GPL license and usable as either an R package or a C++ library, calculates in parallel the distance matrix for different distances/dissimilarities ($$L_1$$

L
1

, $$L_2$$

L
2

, Pearson, cosine and weighted Euclidean) and also implements a parallel fast version of PAM (FASTPAM1) using any data type to reduce memory usage. Moreover, the parallel implementation uses all the cores available in modern computers which greatly reduces the execution time. Besides its general application, the software is especially useful for processing data of single cell experiments. It has been tested in problems including clustering of single cell experiments with up to 289,000 cells with the expression of about 29,000 genes per cell.

Conclusions
Comparisons with other current packages in terms of execution time have been made. The method greatly outperforms the available R packages for distance matrix calculation and also improves the packages that implement the PAM itself. The software is available as an R package at https://CRAN.R-project.org/package=scellpam and as C++ libraries at https://github.com/JdMDE/jmatlib and https://github.com/JdMDE/ppamlib The package is useful for single cell RNA-seq studies but it is also applicable in other contexts where clustering of large data sets is required.
Overestimated prediction using polygenic prediction derived from summary statistics
Authors: Park David Keetae , Chen Mingshen , Kim Seungsoo , Joo Yoonjung Yoonie , Loving Rebekah K. , Kim Hyoung Seop , Cha Jiook , Yoo Shinjae , Kim Jong Hun 
Published: September 2023

Abstract
Background
When polygenic risk score (PRS) is derived from summary statistics, independence between discovery and test sets cannot be monitored. We compared two types of PRS studies derived from raw genetic data (denoted as rPRS) and the summary statistics for IGAP (sPRS).

Results
Two variables with the high heritability in UK Biobank, hypertension, and height, are used to derive an exemplary scale effect of PRS. sPRS without APOE is derived from International Genomics of Alzheimer’s Project (IGAP), which records ΔAUC and ΔR2 of 0.051 ± 0.013 and 0.063 ± 0.015 for Alzheimer’s Disease Sequencing Project (ADSP) and 0.060 and 0.086 for Accelerating Medicine Partnership - Alzheimer’s Disease (AMP-AD). On UK Biobank, rPRS performances for hypertension assuming a similar size of discovery and test sets are 0.0036 ± 0.0027 (ΔAUC) and 0.0032 ± 0.0028 (ΔR2). For height, ΔR2 is 0.029 ± 0.0037.

Conclusion
Considering the high heritability of hypertension and height of UK Biobank and sample size of UK Biobank, sPRS results from AD databases are inflated. Independence between discovery and test sets is a well-known basic requirement for PRS studies. However, a lot of PRS studies cannot follow such requirements because of impossible direct comparisons when using summary statistics. Thus, for sPRS, potential duplications should be carefully considered within the same ethnic group.
Community-wide patterns in pollen and ovule production, their ratio (P/O), and other floral traits along an elevation gradient in southwestern China
Authors: Nepal Shristhi , Trunschke Judith , Ren Zong-Xin , Burgess Kevin S. , Wang Hong 
Published: September 2023

AbstractBackgroundAs the male and female gametophytes of flowering plants, pollen and ovules largely determine the upper and lower boundaries of plant reproductive success. It is commonly predicted that pollen and ovule number per flower should increase, and pollen-ovule ratio (P/O) per flower should decrease with increasing elevation in response to a more stochastic pollination environment. Here, we aimed to determine the response of pollen number, ovule number, and P/O to other floral traits and elevation gradients for 84 insect-pollinated herbaceous flowering plant species in five sub-alpine and alpine communities (2709 to 3896 m a.s.l.) on Yulong Snow Mountain, southwestern China.ResultsSix floral traits, including P/O, floral display area, flower number, tube depth, flower shape, and pollen presentation, were highly correlated with pollen and ovule number per flower. With increasing elevation, pollen number and P/O per flower increased marginally and significantly, respectively; ovule number per individual, flower number per individual, stigma stamen separation, and inflorescence height decreased significantly. However, ovule number per flower and other floral traits (i.e., floral display area, tube depth, stigma height, stamen height, and pollen and P/O per individual) did not change with elevation. We detected significant phylogenetic signals for pollen number, ovule number, and P/O, suggesting that these traits may be highly conserved and with limited response to changing environmental conditions.ConclusionsResults revealed patterns of plant reproductive character evolution along elevation gradients and the potential factors governing their spatial variation in high-elevation environments. Plant species at high elevations are more likely adapted to cross-pollination, indicated by increased P/O per flower at high elevations on Yulong Mountain. Combined effects of phylogenetic history and plant-pollinator interactions should determine plant trait evolution.
Predictive value of intravascular ultrasound for the function of intermediate coronary lesions
Authors: Zhu Yajuan , Zhou Guowei , Yang Lei , Liu Keng , Xie Yuning , Yang Wen-Yi , Dai Qiuyan 
Published: September 2023

AbstractBackgroundIntravascular ultrasound (IVUS) can provide detailed coronary anatomic parameters. The purpose of our study was to evaluate the parameters measured by IVUS for the prediction of intermediate coronary lesions function by referencing quantitative fraction ratio (QFR) ≤ 0.80 (vs. > 0.80).MethodsEighty four cases with 92 intermediate coronary lesions in vessels with a diameter ≥ 2.50 mm were enrolled. Paired assessment of IVUS and cQFR was available, and vessels with cQFR ≤ 0.8 were considered the positive reference standard. Logistic regression was used to select model variables by a maximum partial likelihood estimation test and receiver operating characteristic curve (ROC) analysis to evaluate the diagnostic value of different indices.ResultsPlaque burden (PB) and lesion length (LL) of IVUS were independent risk factors for the function of coronary lesions. The predictive probability P was derived from the combined PB and LL model. The area under the curve (AUC) of PB, (minimum lumen area) MLA, and LL and the predicted probability P are 0.789,0.732,0731, and 0.863, respectively (P < 0.01). The AUC of the predicted probability P was the biggest among them; the prediction accuracy of cQFR ≤ 0.8 was 84.8%, and the sensitivity of the diagnostic model was 0.826, specificity was 0. 725, andP < 0.01.ConclusionPB and LL of IVUS were independent risk factors influencing the function of intermediate coronary lesions. The model combining the PB and LL may predict coronary artery function better than any other single parameter.
Coverage of preventive measures and surveillance for neglected tropical diseases in hard-to-reach communities in Ghana
Authors: Forson Akua Obeng , Awuah Raphael Baffour , Mohammed Abdul Rahim , Owusu-Asenso Christopher Mfum , Akosah-Brempong Gabriel , Abdulai Anisa , Sraku Isaac Kwame , Dhikrullahi Shittu B. , Atakora Sefa Bonsu , Attah Simon K. , Afrane Yaw Asare 
Published: September 2023

Abstract
Background
Neglected tropical diseases (NTDs) are a major public health burden which mainly affects poor populations living in tropical environments and hard-to-reach areas. The study sought to examine coverage of preventive efforts, and case surveillance for NTDs in hard-to-reach communities in Ghana.

Methods
The study investigated treatment efforts for lymphatic filariasis (LF), and onchocerciasis and schistosomiasis/soil transmitted helminths (SCH/STH) at household level, in difficult-to-access communities in Ghana. A total of 621 households were sampled from 6 communities in the Western, Oti and Greater Accra regions.

Results
Over 95% of the households surveyed were covered under mass drug administration (MDA) campaigns for lymphatic filariasis (LF) and onchocerciasis. More than 80% of households had received at least two visits by community drug distributors under the MDA campaigns in the last two years preceding the study. In addition, over 90% of households in the LF and onchocerciasis endemic communities had at least one member using anthelminthic medications under the MDA campaigns in the 12 months preceding the study. However, households where no member had taken anthelminthic medications in 12 months preceding the study were over 6 times likely to have someone in the household with LF.

Conclusions
This study determined that SCH/STH, LF and onchocerciasis are of serious public health concern in some communities in Ghana. There is an urgent need for holistic practical disease control plan involving both financial and community support to ensure total control of NTDs in difficult-to-access communities is achieved.
Application of PVC pipes as an adjustable bilateral traction device in lower limb fractures
Authors: Sun Hongshuo , Li Peng , Du Gangqiang , Jiang Jianhao , Song Kaikai , Liu Hongzhi , Zhang Xinjun , Jia Long , Zhang Kai , Yang Shuye , Wang Zhigang 
Published: September 2023

Abstract
Objective
To introduce a new type of simple adjustable bilateral bidirectional polyvinyl chloride (PVC) tube traction device and discuss the value of using this device before surgery in patients with lower limb fractures.

Methods
To introduce the manufacturing process of an adjustable bilateral traction device made of PVC pipes. From August 2018 to November 2019, the data of 36 patients with lower limb fractures who were treated with this traction device were retrospectively analysed. The treatment outcomes were analysed, including length of both lower limbs, fracture reduction, lower limb mobility, visual analogue scale (VAS) score, incidence of complications, and patient satisfaction.

Results
All patients were able to move the affected limb immediately after using the device. The patient's pain was significantly reduced, they were able to turn over freely during bed rest, and the length of the affected limb was restored to that of the healthy limb. Thirty-four (94.5%) patients were satisfied with the reduction of the fracture end, 2 (5.5%) patients with tibiofibular fractures showed angular displacement of the fractured end and satisfactory reduction after the position of the bone traction needle was adjusted; 7 (19.5%) patients developed deep vein thrombosis of the affected lower limb during traction; there was no decubitus or vascular nerve injury, and the overall complication rate was 25% (9/36). All the patients and their families were satisfied with the results of this treatment.

Conclusion
The aim of this study is to introduce a new type of traction device. It is advantageous in that it is light weight, low cost, easy to assemble, promotes immediate movement of the affected limb after assembly, improves patient comfort and can be used with a titanium steel needle for MRI examination under traction. In the clinical setting, it has been shown to be suitable for the temporary treatment of patients with lower leg fractures prior to surgery, particularly patients who, for various reasons, require nonsurgical treatment in the short term.
Surgical outcomes of segmental diaphyseal forearm fractures in adults: a small case series on plate osteosynthesis, intramedullary nailing, and other surgical methods
Authors: Kim Dong Hee , Jang Hyo Seok , Kwak Sang Ho , Jung Sung Yoon , Jeon Jong Min , Ahn Tae Young , Lee Sang Hyun 
Published: September 2023

Abstract
Background
Segmental fractures often result from high-energy or indirect trauma that causes bending or torsional forces with axial loading. We evaluated surgical outcomes of patients with forearm segmental diaphyseal fractures.

Methods
We retrospectively analyzed data from patients with forearm segmental fractures for which they underwent surgery at the Pusan National University Trauma Center from March 2013 to March 2022. We also analyzed accompanying injuries, injury severity score (ISS), injury mechanism, occurrence of open fracture, surgical technique, and treatment results.

Results
Fifteen patients were identified, one with bilateral segmental diaphyseal forearm bone fracture, for a total of 16 cases. Nine of the patients were male. The overall mean age was 50 years, and the mean follow-up period was 16.2 months. Six cases who underwent surgery using plate osteosynthesis achieved bone union without length deformity at final follow-up. Three of seven patients who underwent intramedullary nailing alone underwent reoperation due to nonunion. Six cases achieved bone union at final follow-up, three of which showed length deformity. Three patients underwent surgery using a hybrid method of IM nailing, plates, and mini cables. One patient who underwent surgery with a plate and one patient who underwent surgery with IM nailing alone showed nonunion and were lost to follow-up.

Conclusion
Plate osteosynthesis is considered the gold standard for treatment of adult forearm diaphyseal segmental fractures. In this study, IM nailing was associated with high rates of non-union and length deformity. However, the combination of IM nailing and a plate-cable system may be an acceptable alternative in segmental diaphyseal forearm fracture, achieving a union rate similar to that provided by plate fixation.
Clinical study on single-port endoscopic resection via a gasless transaxillary approach in the treatment of breast fibroadenoma in adolescents
Authors: Lu Jing-Yu , Zhang Guo-Liang , Lin Xiao-Jing , Chen Dar-Ren , Zheng Zi-Fang , Chen Yu , Lin Li-sheng 
Published: September 2023

Abstract
Background
Breast fibroadenoma is the most common benign breast tumour. This study aimed to investigate the advantages and disadvantages of endoscopic-assisted resection via a gas-less transaxillary single-port approach for breast fibroadenoma in adolescent patients, compared with a traditional approach.

Methods
The clinical data of 83 patients with breast fibroadenoma treated in our hospital from October 2019 to October 2021 were collected for retrospective analysis. These patients were divided into an endoscopic-assisted surgery (ES) group (n = 39) and a traditional open surgery (OS) group (n = 44) according to the surgical approach. The operative time, intraoperative blood loss, incision length, postoperative complications, and patient satisfaction were compared between the two groups.

Results
The surgical cost was (5.1 ± 0.6) thousand Yuan [(0.7 ± 0.1) thousand US dollars] in the ES group and (3.5 ± 2.7) thousand Yuan [(0.5 ± 0.4) thousand US dollars] in the OS group, showing a statistically significant difference (p < 0.001). There was no significant difference in surgical time, intraoperative blood loss, incision length, or the rate of postoperative complications between the two groups. Stratified analysis revealed that the ES group had a significantly shorter operative time [(57.00 ± 10.26) min vs. (78.27 ± 7.63)] (p < 0.001), a smaller incision length [(3.73 ± 0.34) cm vs. (4.42 ± 0.44) cm] (p < 0.001), and a lower complication incidence rate (11.1% vs. 63.6) (p = 0.011) than the OS group in the cases with a nodule number ≥ 3. The satisfaction score using the BREAST-Q scale indicated that psychosocial well-being and patient satisfaction with the breast in the ES group were significantly superior to those in the OS group [(91.18 ± 3.12) points vs. (87.00 ± 4.45) points and (91.03 ± 6.80) points vs. (84.45 ± 6.06) points, respectively] (p < 0.001).

Conclusion
ES is a safe and effective method for the treatment of fibroadenoma. In patients with multiple fibroadenomas (≥ 3 tumours), ES has a shorter operative time and fewer postoperative complications. ES demonstrates a significant, prominent advantage in cosmetic appearance. However, it should be noted that ES is associated with higher costs than OS.
Diagnostic value of high-risk HPV E6/E7 mRNA in patients with ASCUS
Authors: Jin Xiu , Liu Feifei , Zhang Ya , Ma Yingying , Yang Linqing , Wang Yunfei , Liu Ying 
Published: September 2023

Abstract
Objective
To investigate the infection status of high-risk human papillomavirus (HR-HPV) E6/E7 mRNA in patients with a cytological diagnosis of “atypical squamous cells of undetermined significance” (ASCUS) and to analyze the pathogenic rate of different high-risk HPV subtypes combined with biopsy pathological results to provide a more accurate basis for managing ASCUS patients.

Methods
A total of 1387 patients with ASCUS and HPV E6/E7 mRNA positivity who were referred for colposcopy were retrospectively analyzed. They were divided into HPV16+, 18/45 + and other HR-HPV + groups premenopausal and postmenopausal groups. The pathological results of the biopsy were divided into the LSIL- group (including normal and low-grade squamous intraepithelial lesions) and the HSIL + group (including high-grade squamous intraepithelial lesions and higher lesions). SPSS was used for the analysis.

Results
The age group 31–40 years had the highest level of HPV16+, and HPV18/45 + was the highest in the 41–50 years group. The detection rates of HSIL + in the HPV16+, HPV18/45+, HPV 16/18/45 + and Other HR-HPV + groups were 48.4%, 18.8%, 43.9% and 15.0%, respectively. The infection rates of HPV16/18/45 in postmenopausal and premenopausal women were 42.4% and 34.3%, respectively. In the HPV18/45 group, the incidence of HSIL + was 30.0% in postmenopausal women and 15.0% in premenopausal women (P < 0.01). In the HPV 16 + and Other HR-HPV + groups, the incidence of HSIL + in postmenopausal patients was not significantly different from that in premenopausal patients. The incidence of cervical cancer in postmenopausal patients is significantly higher than that in premenopausal patients.

Conclusions
Colposcopy referral or further biopsy is recommended for all ASCUS patients with HPV16/18/45E6/E7 mRNA positivity and postmenopausal patients with HR-HPVE6/E7 mRNA positivity. For premenopausal ASCUS patients with other HR-HPV E6/E7 mRNA positivity, colposcopy should be performed if possible, depending on the specific situation, to achieve early detection and diagnosis.
Association of inflammatory markers with all-cause mortality and cardiovascular mortality in postmenopausal women with osteoporosis or osteopenia
Authors: Qu Li , Zuo Xiaole , Yu Jing , Duan Ran , Zhao Botao 
Published: September 2023

Abstract
Background
The objective of the present study was to investigate whether associations exist between inflammatory biomarkers and all-cause mortality and cardiovascular disease (CVD) mortality in women with postmenopausal osteoporosis (PMOP) or osteopenia.

Methods
In this retrospective cohort study, data were obtained from the National Health and Nutrition Examination Survey database from the years 2007 to 2010, 2013 to 2014, and 2017 to 2018. The inflammatory biomarkers including neutrophil/lymphocyte ratio (NLR), platelet/lymphocyte ratio (PLR), monocyte/lymphocyte ratio (MLR), neutrophil × platelet/lymphocyte (SII), neutrophil × monocyte/lymphocyte (SIRI), and neutrophil × monocyte × platelet/lymphocyte ratio (AISI) were calculated.

Results
A total of 2,834 women were included, with a median survival of 113.51 (3.15) months. During follow-up, 602 women died of all-cause mortality and 185 women died of CVD. NLR, MLR, SIRI, and AISI were significantly associated with all-cause mortality in postmenopausal women with osteoporosis or osteopenia. NLR, MLR, SIRI, and AISI were related to CVD mortality in postmenopausal women with osteoporosis or osteopenia (All P < 0.05). Based on the results of the subgroup analysis, AISI, SIRI, and MLR were associated with all-cause mortality and CVD mortality in postmenopausal women with PMOP or osteopenia who had a history of CVD and diabetes. AISI, SII, MLR, and NLR were associated with all-cause mortality and CVD mortality in PMOP or osteopenia women with a body mass index (BMI) > 25 kg/m2. PLR was associated with all-cause mortality in PMOP or osteopenia women aged ≥ 65 years.

Conclusion
Inflammatory biomarkers were correlated with mortality risk in the PMOP or osteopenia population. This finding may be helpful for the prognosis management of PMOP or osteopenia in postmenopausal women.