bluuebunny/crossref_metadata_2025_split huggingface dataset:
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life
Authors: Sánchez Reyes Luna L , McTavish Emily Jane , O’Meara Brian 
Published: March 2024

Abstract
Chronograms—phylogenies with branch lengths proportional to time—represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life’s phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life’s synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife’s node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.
Replacing alfalfa hay with a novel alfalfa leaf pellet product (ProLEAF MAX) and/or alfalfa stems (ProFiber Plus) in the diet of developing dairy heifers alters dry matter intake, but does not negatively impact growth or development
Authors: Motsinger Laura A , Young Allen Y , Feuz Ryan , Larsen Ryan , Brady Tevan J , Briggs Reganne K , Reichhardt Caleb C , Pratt Chris , Thornton Kara J 
Published: March 2024

Abstract
Alfalfa is a commonly grown forage in the Intermountain West region of the United States and is often included in the diet of dairy cattle. Alfalfa provides a variety of different nutrients, but the nutrient content of alfalfa varies depending on factors such as the soil, region, cutting, and climate. However, alfalfa leaves tend to have less variation in their nutrient content than alfalfa stems. Fractionating alfalfa may be one way to improve control of nutrients provided when developing a ration for developing dairy heifers. The purpose of this study was to determine whether including fractionated alfalfa in the diet impacts the growth or conception rates of developing dairy heifers. Heifers were allocated to one of three treatments: a control group fed a typical diet (CON; n = 8), a diet that replaced alfalfa with fractionated alfalfa leaf pellets and alfalfa stems (ProLEAF MAX + ProFiber Plus; PLM + PFP; n = 8), or a diet that replaced alfalfa with alfalfa stems (PFP; n = 8) for 85 d. Heifers were fed individually twice daily and weight, hip height (HH), and wither height (WH) were recorded every 14 d. Additionally, blood was collected every 28 d, and conception rates were recorded at the end of the trial. Heifers receiving the PFP diet consumed less dry matter (P = 0.001) than the CON treatment. Analyses were then conducted to determine nutrient intake and heifers receiving the PFP diet also consumed less neutral detergent fiber (P = 0.02), acid detergent fiber (P = 0.02), crude protein (P = 0.001), and net energy for maintenance (P = 0.001) than heifers consuming the CON diet; however, no differences (P &gt; 0.10) were observed between heifers fed the CON and PLM + PFP diets. Analysis of body weight gain over the feeding period showed no difference (P = 0.52) among heifers consuming the different treatment diets. Additionally, treatment did not affect average daily gain (P = 0.49), gain:feed (P = 0.82), HH gain (P = 0.20), or WH gain (P = 0.44) among heifers receiving different diets. Treatment × time altered (P &lt; 0.001) blood urea nitrogen when analyzed as a repeated measure. Total feed cost was lowest (P &lt; 0.001) for the PFP diet and cost of gain tended (P = 0.09) to be increased for the PLM + PFP diet compared to the CON diet. Overall, these data indicate that including alfalfa stems in a developing heifer diet may decrease dry matter intake, lower input costs, and increase profitability, without negatively impacting growth.
The Role of 3D Custom Implants in Upper Extremity Surgery
Authors: Choo Andrew , Richard Marc J. 
Published: March 2024

Summary:
As the technology of three-dimensional (3D) printing becomes more refined and accessible, multiple applications of its use are becoming more commonplace in upper extremity surgery. 3D-printed models have been beneficial in preoperative planning of complex cases of acute trauma or malunions, contributing to spatial understanding or even contouring of implants. Custom guides can also be created to assist intraoperatively with precise placement of osteotomies or arthroplasty implants. Finally, custom 3D implants have been described for cases of bone loss in the upper extremity. This can be for relatively small gaps after malunion correction or extensive defects, typically for trauma or tumor. Articular defects can also be addressed with this technology, although special considerations should be given to the implant design and longevity in these situations. Because of the relatively recent nature of 3D implants, long-term data are lacking. However, they show great promise in an expanding range of challenging clinical indications.
Predictive Value of Cervical Degenerative Quantitative Scoring System on Postoperative Disc Height Loss After Cervical Disc Replacement
Authors: Yan Chunyi , Wang Hong , Abudouaini Haimiti , Wu Tingkui , Wang Beiyu , Liu Hao 
Published: March 2024

Study design:
A retrospective study.

Objective:
In this study, a cervical degenerative quantitative scoring system was used to identify the risk factors for disc height loss after cervical disc replacement (CDR) and to verify their accuracy.

Background:
Disc height loss after CDR is drawing much attention. Preoperative cervical degeneration has been proven related to postoperative disc height loss but lacked quantitative verification.

Patients and Methods:
A total of 160 patients who underwent CDR with the Prestige-LP disc at our hospital between January 2011 and December 2016 were retrospectively reviewed. Disc height loss was defined as a reduction of more than 2 mm from postoperative to the final follow-up. A quantitative scoring system was used to evaluate preoperative degeneration on radiographs. Multivariate logistic regression was applied to determine predictive factors and calculate the logistic regression formula. Moreover, receiver operating characteristic curve analysis was conducted to obtain the optimal cutoff value and the area under the receiver operating characteristic curve [areas under the curve (AUC)].

Results:
Study subjects had a mean age of 43.51 ± 8.51 years, with a mean follow-up time of 60.14 ± 12.75 months. The overall incidence rate of disc height loss was 65.62%. Multivariate logistic regression analysis showed that endplate sclerosis (P = 0.000) and low preoperative disc height (P = 0.000) were independent risk factors for postoperative disc height loss. In addition, the calculated optimal cutoff point was 1 point of endplate sclerosis (AUC = 0.768) and 4.5 mm of preoperative disc height (AUC = 0.795). The regression formula established by multivariate logistic regression analysis was composed of preoperative disc height (odds ratio: 2.995, P = 0.000) and endplate sclerosis (odds ratio: 18.131, P = 0.000), with an AUC of 0.879.

Conclusions:
Our findings suggest that a comprehensive preoperative assessment is essential when patients with apparent endplate sclerosis and low preoperative disc height are being considered for CDR.
Development of a Novel Risk Stratification Score to Predict 30-Day Mortality in Cervical Trauma Patients
Authors: Cartagena-Reyes Miguel A. , Solomon Eric , Silva Aponte Juan , Joshi Aditya , Raad Micheal , Hassanzadeh Hamid , Jain Amit 
Published: March 2024

Study Design:
Case control.

Objective:
Traumatic cervical spine injuries are associated with a substantial risk of mortality. The aim of this study is to develop a novel mortality prediction model for patients with cervical trauma who require operative treatment.

Summary of Background Data:
Patients with cervical spine trauma have a high risk of postoperative complications and mortality. There are few reliable systems that can accurately predict mortality after surgery for cervical spine trauma, and those that do exist are typically not specific to cervical trauma.

Materials and Methods:
The National Surgical Quality Improvement Program (NSQIP) database was used to identify patients undergoing surgery for cervical spine trauma. Univariate analyses were performed to identify variables associated with mortality. Variables that were found to be significant in the univariate models were compiled into a multivariable model. The final model was compared with the American Society of Anesthesiologists (ASA), a modified Charlson comorbidity index (mCCI), and the 5-factor modified frailty index (mFI-5) in respect to predicting 30-day mortality after cervical trauma. The score was then externally validated using the Nationwide Inpatient Sample (NIS) database.

Results:
Fifty-five (6.7%) of 822 patients did not survive 30 days after surgery. The final multivariable logistic regression model consisted of the following variables: circumferential fusion “C.” long “L” fusion (more than 4 levels), anemia “A,” age over 60 “A,” and dialysis “D.” The risk of mortality increased with increasing CLAAD score, with mortality rates of 0.9%, 3.1%, 7.4%, 22.7%, and 14.3% for scores of 0, 1, 2, 3, and 4, respectively. The CLAAD model had an AUC of 0.73 for predicting mortality after cervical trauma.

Conclusions:
The CLAAD score is a simple and effective system that can help identify patients at risk of increased mortality within 30 days of cervical trauma.

Level of Evidence:
Level III.
Radiology Reports Do Not Accurately Portray the Severity of Cervical Neural Foraminal Stenosis
Authors: Lee Yunsoo , Ziad Issa Tariq , Mazmudar Aditya S. , Tarawneh Omar H. , Toci Gregory R. , Lambrechts Mark J. , DiDomenico Eric J. , Kwak Daniel , Becsey Alexander N. , Henry Tyler W. , Haider Ameer A. , Larkin Collin J. , Kaye Ian David , Kurd Mark F. , Canseco Jose A. , Hilibrand Alan S. , Vaccaro Alexander R. , Kepler Christopher K. , Schroeder Gregory D. 
Published: March 2024

Study Design:
Retrospective study.

Objective:
(1) To compare cervical magnetic resonance imaging (MRI) radiology reports to a validated grading system for cervical foraminal stenosis (FS) and (2) to evaluate whether the severity of cervical neural FS on MRI correlates to motor weakness or patient-reported outcomes.

Background:
Radiology reports of cervical spine MRI are often reviewed to assess the degree of neural FS. However, research looking at the association between these reports and objective MRI findings, as well as clinical symptoms, is lacking.

Patients and Methods:
We retrospectively identified all adult patients undergoing primary 1 or 2-level anterior cervical discectomy and fusion at a single academic center for an indication of cervical radiculopathy. Preoperative MRI was assessed for neural FS severity using the grading system described by Kim and colleagues for each level of fusion, as well as adjacent levels. Neural FS severity was recorded from diagnostic radiologist MRI reports. Motor weakness was defined as an examination grade <4/5 on the final preoperative encounter. Regression analysis was conducted to evaluate whether the degree of FS by either classification was related to patient-reported outcome measure severity.

Results:
A total of 283 patients were included in the study, and 998 total levels were assessed. There were significant differences between the MRI grading system and the assessment by radio-logists (P < 0.001). In levels with moderate stenosis, 28.9% were classified as having no stenosis by radiology. In levels with severe stenosis, 29.7% were classified as having mild-moderate stenosis or less. Motor weakness was found similarly often in levels of moderate or severe stenosis (6.9% and 9.2%, respectively). On regression analysis, no associations were found between baseline patient-reported outcome measures and stenosis severity assessed by radiologists or MRI grading systems.

Conclusion:
Radiology reports on the severity of cervical neural FS are not consistent with a validated MRI grading system. These radiology reports underestimated the severity of neural foraminal compression and may be inappropriate when used for clinical decision-making.

Level of Evidence:
Level III.
Impact of Weekday on Short-term Surgical Outcomes After Lumbar Fusion Surgery
Authors: Heard Jeremy C. , Ezeonu Teeto , Lee Yunsoo , Narayanan Rajkishen , Issa Tariq , McCall Cordero , Dulitzki Yoni , Resnick Dylan , Zucker Jeffrey , Shaer Alexander , Kurd Mark , Hilibrand Alan S. , Vaccaro Alexander R. , Kepler Christopher K. , Schroeder Gregory D. , Canseco Jose A. 
Published: March 2024

Study Design:
Retrospective cohort study.

Objective:
The purpose of this study is to investigate whether weekday lumbar spine fusion surgery has an impact on surgical and inpatient physical therapy (PT) outcomes.

Summary of Background Data:
Timing of surgery has been implicated as a factor that may impact outcomes after spine surgery. Previous literature suggests that there may be an adverse effect to having surgery on the weekend.

Methods:
All patients ≥18 years who underwent primary lumbar spinal fusion from 2014 to 2020 were retrospectively identified. Patients were subdivided into an early subgroup (surgery between Monday and Wednesday) and a late subgroup (surgery between Thursday and Friday). Surgical outcome variables included inpatient complications, 90-day readmissions, and 1-year revisions. PT data from the first inpatient PT session included hours to PT session, AM-PAC Daily Activity or Basic Mobility scores, and total gait trial distance achieved.

Results:
Of the 1239 patients identified, 839 had surgery between Monday and Wednesday and 400 had surgery between Thursday and Friday. Patients in the later surgery subgroup were more likely to experience a nonsurgical neurologic complication (3.08% vs. 0.86%, P=0.008); however, there was no difference in total complications. Patients in the early surgery subgroup had their first inpatient PT session earlier than patients in the late subgroup (15.7 vs. 18.9 h, P<0.001). However, patients in the late subgroup achieved a farther total gait distance (98.2 vs. 75.4, P=0.011). Late surgery was a significant predictor of more hours of PT (est.=0.256, P=0.016) and longer length of stay (est.=2.277, P=0.001). There were no significant differences in readmission and revision rates.

Conclusions:
Patients who undergo surgery later in the week may experience more nonsurgical neurologic complications, longer wait times for inpatient PT appointments, and longer lengths of stay. This analysis showed no adverse effect of later weekday surgery as it relates to total complications, readmissions, and reoperations.

Level of Evidence:
Level III.
Management of massive hemothorax resulting from traumatic diaphragm rupture with kidney avulsion injury by combined anterior thoracoabdominal approaches
Authors: Lin Keng-Li , Lin Heng-Fu , Tseng Yi-Shiou , Wu Chien , Wang Hu-Lin Christina 
Published: March 2024

Abstract
Blunt trauma resulting in diaphragm rupture, kidney avulsion injury, and subsequent hemothorax is rare and requires immediate surgical intervention. After diagnosis, urgent laparotomy with thoracotomy is needed to control renal bleeding. However, because of limitations in imaging studies, confirming this diagnosis is not straightforward, thus underscoring the importance of proper patient’s posturing. It is recommended that in cases of massive hemothorax combined with intra-abdominal bleeding, no matter performing thoracotomy or laparotomy first, the attending surgeons have to put patients in a position appropriate for simultaneous thoracoabdominal approach. It avoids surgical delays that could lead to fatal outcomes.
Impact of Body-contouring Surgery Post Bariatric Surgery on Patient Well-being, Quality of Life, and Body Image: Saudi Arabia-based Cross-sectional Study
Authors: Neel Omar Fouda , Algaidi Yaser , Alsubhi Mohammed Naif , Al-Terkawi Reem Abdulmonem , Salem Abdelrahman , Mortada Hatan 
Published: March 2024

Background:
Body-contouring surgery is commonly performed to address functional and aesthetic issues that can arise following bariatric surgery. However, there is limited understanding of the psychological impact of this procedure on Saudi Arabian patients who have undergone bariatric surgery. This study aimed to explore the effects of body-contouring surgery on the psychological well-being, quality of life, and body image of individuals who have undergone bariatric surgery.

Methods:
This cross-sectional study assessed the psychological impact of body-contouring surgery by measuring levels of depression and generalized anxiety disorder using the Patient Health Questionnaire-9 (PHQ-9) and the Generalized Anxiety Disorder-7 (GAD-7) scale, respectively.

Results:
The study included a total of 227 participants, with 112 (49.3%) undergoing body-contouring surgery. Among the entire sample, 77.5% experienced excess skin folds following bariatric surgery. The prevalence of depression was 6% in the body-contouring group, lower than the 8% observed in the non–body-contouring group (P = 0.073). Notably, anxiety was significantly lower in the body-contouring group, with a prevalence of 4% compared with 6% in the non–body-contouring group (P = 0.006). Additionally, patients who had undergone body-contouring surgery reported higher scores for emotional well-being when compared with those who had not undergone body-contouring (P = 0.011).

Conclusions:
The study suggests that body-contouring surgery improves the physical appearance of bariatric-surgery patients and reduces anxiety and depression, leading to improved psychological well-being. Further research, including larger and more diverse populations, such as multicenter studies at a regional or international level, is needed to validate these findings.
Experiences of Workplace Violence in Graduate Nursing Clinical Education
Authors: Gigli Kristin H. , Gonzalez John D. 
Published: March 2024

Background:
Exposure to workplace violence (WPV) is common in health care, and little is known about nurse practitioner (NP) students’ experiences during graduate nursing clinical education.

Purpose:
This study described experiences of WPV among NP students during their clinical education.

Methods:
We conducted a cross-sectional, quantitative survey of a random sample of NPs licensed in Texas examining graduate nursing education experiences.

Results:
A total of 334 NPs responded, a 12% response rate. More than a quarter (27%) experienced WPV during their graduate nursing clinical experience. Preceptors were the most reported perpetrators (44%). Most NPs remained in their clinical site after their WPV experience (55%); a majority felt they had no alternative clinical placement option.

Conclusions:
Nurse practitioner students experience WPV, and there may be implications for educational persistence and their careers. Future work should attempt to reduce the frequency of student WPV experiences and examine implications for NP careers.
A Novel EPC1::KDM2B Fusion in High-grade Endometrial Stromal Sarcoma
Authors: Vroobel Katherine M. , Khalid Sana , Cavalchini Silvia , Attygalle Ayoma D. 
Published: March 2024

The spectrum of endometrial stromal sarcoma (ESS) has expanded substantially since the publication of the most recent World Health Organisation (WHO) Classification of Female Genital Tumours and the advent of widely available genomic testing. We describe a uterine mesenchymal tumor harboring a novel EPC1::KDM2B fusion, best classified within the umbrella of high-grade endometrial stromal sarcoma (HGESS). This tumor was composed of a uniform population of spindled cells with some myxoid stroma, a mitotic rate of up to 21/10 high-power fields, and a largely pushing margin with focal vascular invasion. Immunohistochemistry showed strong and diffuse cyclin D1 positivity while CD10, WT1, DOG1, CD117, CD34, CD99, S100, MelanA, SMA, desmin, and h-caldesmon were negative. The tumor was confined to the uterus and no recurrence has been detected thus far, albeit with a short follow-up interval of 9 mo.
Macrophage polarization disorder in the endometrial immune microenvironment may contribute to recurrent implantation failure
Authors: Liu Yun , Tan Xian-Ming , He Tian-Tian 
Published: March 2024

Objective:
To investigate the role and mechanisms by which macrophages (MΦ) contribute to the immune environment of the endometrium in cases of recurrent implantation failure (RIF).

Methods:
Endometrial transcriptome data from women with and without RIF (control group) were collected. The CIBERSORT software was used to determine the abundance of immune cells within the endometrial tissue based on expression profiles. Weighted gene co-expression network analysis was used to identify crucial regulatory genes and pathways.

Results:
Application of CIBERSORT confirmed significant infiltration of macrophages in the RIF group. SOX6, TTC21A, KLHL31, NFIA, TNNT1, TPM1, CPVL, FUS, PEX5, and SLC43A3 were all closely correlated with M2 and M0 macrophages. Metascape and DisNor analyses revealed that these genes contribute to the regulation of macrophage polarization via the Wnt signaling pathway.

Conclusion:
This study identified dysregulation of macrophage polarization within the immune microenvironment of the endometrium in patients with RIF. A comprehensive analysis was conducted to investigate the potential mechanisms underlying this disorder. Dysregulation of macrophage polarization in the endometrium of patients with RIF is strongly associated with the Wnt signaling pathway.