bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes
Authors: Wang Meng , Banik Ishani , Shain A. Hunter , Yeh Iwei , Bastian Boris C. 
Published: June 2022

Abstract
Background
Acral and mucosal melanomas are aggressive subtypes of melanoma, which have a significantly lower burden of somatic mutations than cutaneous melanomas, but more frequent copy number variations, focused gene amplifications, and structural alterations. The landscapes of their genomic alterations remain to be fully characterized.

Methods
We compiled sequencing data of 240 human acral and mucosal melanoma samples from 11 previously published studies and applied a uniform pipeline to call tumor cell content, ploidy, somatic and germline mutations, as well as CNVs, LOH, and SVs. We identified genes that are significantly mutated or recurrently affected by CNVs and implicated in oncogenesis. We further examined the difference in the frequency of recurrent pathogenic alterations between the two melanoma subtypes, correlation between pathogenic alterations, and their association with clinical features.

Results
We nominated PTPRJ, mutated and homozygously deleted in 3.8% (9/240) and 0.8% (2/240) of samples, respectively, as a probable tumor suppressor gene, and FER and SKP2, amplified in 3.8% and 11.7% of samples, respectively, as probable oncogenes. We further identified a long tail of infrequent pathogenic alterations, involving genes such as CIC and LZTR1. Pathogenic germline mutations were observed on MITF, PTEN, ATM, and PRKN. We found BRAF V600E mutations in acral melanomas with fewer structural variations, suggesting that they are distinct and related to cutaneous melanomas. Amplifications of PAK1 and GAB2 were more commonly observed in acral melanomas, whereas SF3B1 R625 codon mutations were unique to mucosal melanomas (12.9%). Amplifications at 11q13-14 were frequently accompanied by fusion to a region on chromosome 6q12, revealing a recurrent novel structural rearrangement whose role remains to be elucidated.

Conclusions
Our meta-analysis expands the catalog of driver mutations in acral and mucosal melanomas, sheds new light on their pathogenesis and broadens the catalog of therapeutic targets for these difficult-to-treat cancers.
The prevention of gestational diabetes mellitus (The role of lifestyle): a meta-analysis
Authors: Altemani Abdullah H. , Alzaheb Riyadh A. 
Published: June 2022

AbstractGestational diabetes mellitus (GDM) is the most common complication of pregnancy. The disease is on the rise worldwide with deleterious consequences on the fetus, mother, and children. The study aimed to review the role of lifestyle in the prevention of GDM. We searched PubMed, SCOPUS, Web of Science, Cochrane Library, EBSCO, and Google Scholar from the first published article up to December 2021; articles were eligible if they were controlled trials, prospective cohorts, and case–control. Out of 5559 articles retrieved, 66 full texts were screened, and 19 studies were included in the meta-analysis. (6 studies assessed the effects of diet, and 13 were on exercise). The dietary intervention showed significant positive effect on GDM, odd ratio = 0.69, 95% CI, 0.56–84, P-value for overall effect = 0.002. The DASH diet was better than Mediterranean Diet (odd ratio, 0.71, 95% CI, 68–74, P-value < 0.001). Regarding exercise, no significant prevention was evident on GDM, odd ratio, 0.77, 95% CI, 0.55–1.06, P-value = 0.11. However, a significant prevention of gestational diabetes was found when the exercise was mild-moderate (odd ratio = 0.65, 95% CI, 0.53–80, P < 0.0001) and started in the first trimester (odd ratio, 0.57, 95% CI, 0.43–0.75, P < 0.0001. No significant effect was found when the exercise was vigorous (odd ratio = 1.09, 95% CI, 0.50–2.38, P = 0.83) and started during the second trimester of pregnancy (odd ratio, 1.08, 95% CI, 0.65–1.80, P = 0.77. Diet and early mild-moderate exercise were effective in GDM prevention. Exercise during the second trimester and moderate-vigorous were not. Further studies assessing the type, duration, and frequency of physical activity are needed.
Cross-sectional chest circumference and shape development in infants
Authors: Seifnaraghi Nima , de Gelidi Serena , Frerichs Inéz , Kallio Merja , Sorantin Erich , Tizzard Andrew , Demosthenous Andreas , Bayford Richard H. 
Published: June 2022

Abstract
Objective
This study investigates the development of the thoracic cross-section at the nipple line level during the early stages of life. Unlike the descriptive awareness regarding chest development course, there exist no quantitative references concerning shape, circumference and possible dependencies to age, gender or body weight. The proposed mathematical relations are expected to help create guidelines for more realistic modelling and potential detection of abnormalities. One potential application is lung electrical impedance tomography (EIT) monitoring where accurate chest models are crucial in both extracting reliable parameters for regional ventilation function and design of EIT belts. Despite their importance, such reference data is not readily available for the younger age range due to insufficient data amid the regulations of neonatal imaging.

Results
Chest circumference shows the highest correlation to body weight following the relation $$f\left(x\right)= 18.3735 \ \mathrm{ln}\left(0.0012x+2.1010\right)$$

f

x

=
18.3735

ln

0.0012
x
+
2.1010

where x is the body weight in grams and f(x) is the chest circumference in cm at the nipple line level. No statistically significant difference in chest circumference between genders was detected. However, the shape indicated signs of both age and gender dependencies with on average boys developing a more rectangular shape than girls from the age of 1 years and 9 months.
Superior peroneal retinaculum reattachment for an atraumatic peroneus brevis tendon subluxation: a case report
Authors: Grandberg Camila , de Oliveira Diovano Paust , Gali Julio Cesar 
Published: June 2022

Abstract
Background
Peroneal tendon subluxation is a rare pathology, generally associated with sport-induced trauma, that occurs due to the rupture of the superior peroneal retinaculum. The diagnosis is mainly clinical, but the use of imaging techniques, such as dynamic ultrasound and magnetic resonance imaging, may contribute to its clarification. Treatment may be conservative or surgical, although there is no consensus on the most appropriate technique to be employed. We report a case of subluxation of the peroneus brevis tendon, with no apparent traumatic cause, in which there was a need for a surgical approach after the failure of conservative treatment.

Case presentation
A 25-year-old White woman presented pain and locking of the lateral side of the left foot 2 years earlier, with no history of trauma. The patient felt pain upon palpation and presented snapping during flexion–extension of the left ankle. On dynamic ultrasonography, an anterior subluxation of the peroneus brevis tendon occurred when the ankle was in dorsiflexion, suggesting superior peroneal retinaculum injury. Surgical correction was recommended after 2 months of conservative treatment with no improvement. The chosen surgical technique was isolated reattachment of the superior peroneal retinaculum, which proved successful.

Conclusions
Peroneal tendon subluxation has no established preferred surgical technique. This case demonstrates superior peroneal retinaculum repair as an efficient surgical approach for this condition. Furthermore, the atraumatic mechanism of injury in this case, along with the unknown true incidence of peroneal tendon subluxation, highlights the need to consider this pathology in cases of ankle injuries.
Sex differences in the human metabolome
Authors: Costanzo Michele , Caterino Marianna , Sotgiu Giovanni , Ruoppolo Margherita , Franconi Flavia , Campesi Ilaria 
Published: June 2022

Abstract
Background
The sexual dimorphism represents one of the triggers of the metabolic disparities between the organisms, advising about wild implications in research or diagnostics contexts. Despite the mounting recognition of the importance of sex consideration in the biomedical fields, the identification of male- and female-specific metabolic signatures has not been achieved.

Main body
This review pointed the focus on the metabolic differences related to the sex, evidenced by metabolomics studies performed on healthy populations, with the leading aim of understanding how the sex influences the baseline metabolome. The main shared signatures and the apparent dissimilarities between males and females were extracted and highlighted from the metabolome of the most commonly analyzed biological fluids, such as serum, plasma, and urine. Furthermore, the influence of age and the significant interactions between sex and age have been taken into account.

Conclusions
The recognition of sex patterns in human metabolomics has been defined in diverse biofluids. The detection of sex- and age-related differences in the metabolome of healthy individuals are helpful for translational applications from the bench to the bedside to set targeted diagnostic and prevention approaches in the context of personalized medicine.

Graphical Abstract
Damaged glyptodontid skulls from Late Pleistocene sites of northwestern Venezuela: evidence of hunting by humans?
Authors: Carlini Alfredo A. , Carrillo-Briceño Jorge D. , Jaimes Arturo , Aguilera Orangel , Zurita Alfredo E. , Iriarte José , Sánchez-Villagra Marcelo R. 
Published: June 2022

AbstractThe Muaco and Taima-Taima sites, in Falcón State of northwestern Venezuela, are among the earliest sites of human occupation in South America containing artifacts associated with preserved megafaunal remains and dating between 19,810 and 15,780 calybp. Here we report novel visual and CT scanning analysis of six glyptodont skulls of Glyptotherium cf. cylindricum from these sites, of which four exhibit distinct and similar patterns of breakages in the fronto-parietal region that suggest intentional blows by direct percussion by humans, with fractures not being diagenetic but instead antemortem or transmortem. This hypothesized and unreported hunting technique focused in an area of the skull where the cephalic shield becomes thin, thus increasing the effectiveness of the blow. From Taima-Taima other glyptodont remains included an inverted carapace, also previously reported as probable evidence of human–glyptodont interaction during the latest Pleistocene. We estimated that roughly 150-170 Kg of potentially accessible muscles and fat of an adult Glyptotherium cylindricum could be used as food sources.
Evaluation of antimicrobial and cytotoxic effects of Echinacea and Arctium extracts and Zataria essential oil
Authors: Yazdanian Mohsen , Rostamzadeh Pouya , Alam Mostafa , Abbasi Kamyar , Tahmasebi Elahe , Tebyaniyan Hamid , Ranjbar Reza , Seifalian Alexander , Moghaddam Mehrdad Moosazadeh , Kahnamoei Majid Balaei 
Published: June 2022

AbstractDental caries and oral infections have become a widespread issue in the modern world. This study aimed to investigate the antibacterial, antifungal, and cytotoxicity characteristics of the extracts ofEchinacea purpura,Arctium lappa, and the essential oil ofZataria multifloraas a potential herbal mouthwash. The essential oil ofZ. multifloraleaves and the extracts ofE. purpurea and A. lapparoots were prepared. The characterization was carried out by GC-MS and also, total phenol and flavonoid were assed for all three samples. The antimicrobial and anti-biofilm effects were evaluated againstStreptococcus mutans, Streptococcus mitis, Streptococcus salivarius, Lactobacillus acidophilus, Escherichia coli, Staphylococcus aureus,andCandida albicans.The cytotoxic effect of the samples was evaluated on HEK 293 and HDFa cells by MTT test. Thymol and carvacrol contents in EO ofZ. multiflorawere measured at 31% and 42.2%, respectively.A. lappahad the lowest total phenolic and flavonoid value among the samples. On the other hand, the total phenolic content ofZ. multifloraand the total flavonoid content ofE. purpureawere the highest. The MIC values ofZataria,Arctium, andEchinaceaagainstS. mutanswere 0.011% v/v, 187.5 mg/ml, and 93.75 mg/ml, while MBC were 0.011% v/v, 375 mg/ml, and 187.5 mg/ml, respectively. The formulation showed bactericidal activity againstS. mutansin the concentration of 5.86 mg/ml for Echinacea and Burdock extracts and 0.08 µl/ml for EO ofZataria.The formulation significantly affected microbial biofilm formation and induced biofilm degradation. The cell viability percentages were higher than 50% during 24 and 48 h. The formulation had a significant antimicrobial effect on cariogenic bacteria andC. albicans, with the lowest cytotoxic effects. Therefore, this formulation can be an appropriate candidate for mouthwash.
Identification of peroxiredoxin II and its related molecules as potential biomarkers of dermal mesenchymal stem cell homing using network analysis
Authors: Han Ying-Hao , Mao Ying-Ying , Feng Yao-Yuan , Xiang Hong-Yi , Sun Hu-Nan , Jin Mei-Hua , Kwon Taeho 
Published: June 2022

AbstractIn this study, we performed RNA sequencing of Prx II+/+ and Prx II−/− dermal mesenchymal stem cells (DMSCs) to identify differentially expressed genes (DEGs). To explore the role of Prx II in DMSCs, we performed Gene Ontology analysis of the DEGs. The results showed that the DEGs were mainly involved in the biological processes of cell migration, intercellular adhesion, and coordination of the regulation of stem cell homing. Through the construction of protein–protein interaction network, four hub genes Cd274, Ccl5, Il1b, and Stat1 involved in cell adhesion and cell homing were screened. Quantitative reverse transcription PCR analysis showed that Cd274, Ccl5, Il1b, and Stat1 were down regulated in Prx II−/− DMSCs. miRwalk and Starbase databases were further used to screen the upstream molecules miRNA and lncRNA regulating hub gene. Prx II was found to be involved in the regulation of stem cell homing via the Tctn2/miR-351/Stat1/Il1b axis. Thus, we demonstrated that Prx II is a key molecule in the regulation of the homing ability of DMSCs. Our results provide a theoretical foundation for improving the homing ability of DMSCs by targeting Prx II.
Evaluation of Mechanical Characteristics of High-Strength Reinforced Concrete Columns with Hexagonal Chicken Wire Mesh Under Cyclic Loading
Authors: Bastami Morteza , Mousavi Ahmad Elmi , Abbasnejadfard Mostafa 
Published: June 2022

AbstractRecently, new materials and methods have been implemented to improve the performance of reinforced concrete columns. This paper studies experimentally the behavior of reinforced high-strength columns, with additional internal confinement using hexagonal chicken wire mesh (HCWM) to enhance ductility, energy absorption, and ultimate strength and reduce the brittleness of traditional columns. Eight double-ended one-third-scale columns with different volumetric ratios of transverse rebar have been constructed and loaded under the uniform axial compression and lateral cyclic loads. Different volumetric ratios of transverse rebar were provided based on special, intermediate, and ordinary moment frames specifications of ACI 318–14 (named SD, ID, and OD, respectively). The specimens were confined by transverse rebars and HCWM and the results were compared with reference specimens with traditional transverse ties. Experimental findings demonstrated that HCWM specimens exhibited better performance compared to their control specimens concerning crack control efficiency, load capacity, ductility, energy dissipation, and failure modes. Implementation of HCWM increased the ultimate deformation, ductility, and energy absorption of OD specimens up to 21%, 50%, and 175%, respectively, compared to their control specimen. Confinement of the concrete columns by HCWM increased the ultimate strength of OD and ID specimens up to 15% and 22% under the cyclic load, but has a negligible effect on SD columns due to enough ratio of transverse and longitudinal rebars in SD specimens. As a result, confinement of specimens by HCWM could be regarded as a simple and effective method to improve the seismic characteristics of RC columns, particularly those members constructed with a minimal number of transverse rebars.
Heat stress impacts the multi-domain ruminal microbiota and some of the functional features independent of its effect on feed intake in lactating dairy cows
Authors: Park Tansol , Ma Lu , Gao Shengtao , Bu Dengpan , Yu Zhongtang 
Published: June 2022

Abstract
Background
Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime).

Results
The HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relative abundance of Bacteroidetes (primarily Gram-negative bacteria) while decreasing that of Firmicutes (primarily Gram-positive bacteria) and the Firmicutes-to-Bacteroidetes ratio. Some genera were exclusively found in the heat-stressed cows and thermal control cows. Some co-occurrence and mutual exclusion between some genera were also found exclusively for each thermal condition. Heat stress did not significantly affect the overall functional features predicted using the 16S rRNA gene sequences and ITS1 sequences, but some enzyme-coding genes altered their relative abundance in response to HS.

Conclusions
Overall, HS affected the prokaryotes, fungi, and protozoa of the ruminal microbiota in lactating Holstein cows to a different extent, but the effect on the structure of ruminal microbiota and functional profiles was limited when not confounded by the effect on feed intake. However, some genera and co-occurrence were exclusively found in the rumen of heat-stressed cows. These effects should be attributed to the direct effect of heat stress on the host metabolism, physiology, and behavior. Some of the “heat-stress resistant” microbes may be useful as potential probiotics for cows under heat stress.
The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine
Authors: Herremans Kelly M. , Riner Andrea N. , Cameron Miles E. , McKinley Kelley L. , Triplett Eric W. , Hughes Steven J. , Trevino Jose G. 
Published: June 2022

AbstractPancreatic cancer is a deadly disease with limited diagnostic and treatment options. Not all populations are affected equally, as disparities exist in pancreatic cancer prevalence, treatment and outcomes. Recently, next-generation sequencing has facilitated a more comprehensive analysis of the human oral microbiome creating opportunity for its application in precision medicine. Oral microbial shifts occur in patients with pancreatic cancer, which may be appreciated years prior to their diagnosis. In addition, pathogenic bacteria common in the oral cavity have been found within pancreatic tumors. Despite these findings, much remains unknown about how or why the oral microbiome differs in patients with pancreatic cancer. As individuals develop, their oral microbiome reflects both their genotype and environmental influences. Genetics, race/ethnicity, smoking, socioeconomics and age affect the composition of the oral microbiota, which may ultimately play a role in pancreatic carcinogenesis. Multiple mechanisms have been proposed to explain the oral dysbiosis found in patients with pancreatic cancer though they have yet to be confirmed. With a better understanding of the interplay between the oral microbiome and pancreatic cancer, improved diagnostic and therapeutic approaches may be implemented to reduce healthcare disparities.
Moving wildlife tracking forward under forested conditions with the SWIFT GPS algorithm
Authors: Forrest S. W. , Recio M. R. , Seddon P. J. 
Published: June 2022

AbstractThe remote collection of animal location data has proliferated in recent decades, and higher-frequency data are increasingly available with battery-saving optimisations such as ‘snapshot’ algorithms that acquire GPS satellite data and post-process locations off-board. This is the first study to assess the effects of vegetation and topography on the fix success rate and location error of global positioning system (GPS) devices that use the SWIFT fix algorithm, developed by Lotek. To assess fix success rate (FSR—the proportion of successful fixes compared to the total number of attempts) and location error (LE), we conducted a stationary test at a predominately forested site on the South Island of New Zealand. The overall FSR was 83% (± 15.3% SD), which was affected strongly by canopy closure above 90%. Half of the locations were within 8.65 m of the true location, 79.7% were within 30 m, and 95% of locations were within 271 m. When 6 or more satellites were used, this reduced to 4.92 m and 18.6 m for 50% and 95%, respectively. Horizontal dilution of precision (HDOP), the number of satellites, and canopy closure all influenced location error. To field test the fix success rate of SWIFT GPS devices, we deployed them on forest-dwelling parrots with 2 and 3-h fix intervals, which showed similar FSR results to the stationary test when cavity-nesting individuals were removed (FSR mean ± SD = 81.6 ± 5.0%). The devices lasted an average of 147 days before depleting the battery, resulting in an average of 1087 successful fixes per individual at an average time of 9.38 s to acquire the GPS ephemeris, resulting in an average of 3.73 attempted locations per mAh of battery for PinPoint 350 devices. Our study provides a baseline for fix success rates and location errors under forested conditions that can be used for future SWIFT GPS tracking studies.