bluuebunny/crossref_metadata_2025_split huggingface dataset:
Esophageal disease and loss to follow-up are common among patients who experience non-endoscopic resolution of food impaction
Authors: Hoversten Patrick , Lomeli Luis , Broman Aimee Teo , Gaumnitz Eric , Hillman Luke 
Published: August 2022

SummaryMany patients who experience esophageal food impaction (EFI) will have non-endoscopic resolution (NER) of their EFI, but this population is poorly defined. The purpose of this study is to describe the outcomes of patients with NER of EFI. A retrospective chart review from 2007 to 2017 was performed at a single tertiary care center. There were 593 patients who presented to the emergency department with EFI, defined as recent soft food ingestion and inability to tolerate oral secretions. Adequate follow-up was defined as a gastroenterology clinic visit or EGD within 6 months of EFI. Out of these, 149 patients (25.1%) had NER of their EFI. Patients with NER were less likely to have adequate follow-up than those with ER (45.0% vs. 59.5%, P = 0.003). Of those without established esophageal disease and NER, 92.5% had significant esophageal pathology on endoscopy, including stricture (34.0%), features of eosinophilic esophagitis (30.2%), and esophagitis (22.6%). Recurrent EFI occurred at a similar rate between patients with NER and ER (9.4% vs. 14.6%, P = 0.14). Patients with established esophageal disease (odds ratio [OR]: 1.51, P = 0.04) and recommendation to follow-up at time of EFI (OR: 6.06, P &lt; 0.001) were most likely to follow up after EFI. Approximately, a quarter of patients with EFI will experience NER of their EFI. Virtually, all patients (92.5%) were found to have esophageal disease warranting longitudinal care. Importantly, follow-up rates are significantly lower in those with NER than their counterparts requiring EGD. Our study highlights the need to develop standardized protocols that improve follow-up for patients after NER of EFI.
Changes in Burn Surgery Operative Volume and Metrics due to COVID-19
Authors: Yoon Joshua S , Khoo Kimberly H , Akhavan Arya A , Lagziel Tomer , Ha Michael , Cox Carrie A , Blanding Renee , Werthman Emily H , Caffrey Julie , Hultman C Scott 
Published: August 2022

AbstractDue to COVID-19, hospitals underwent drastic changes to operating room policy to mitigate the spread of the disease. Given these unprecedented measures, we aimed to look at the changes in operative volume and metrics of the burn surgery service at our institution. A retrospective review was conducted for operative cases and metrics for the months of March to May for 2019, 2020, and 2021, which correspond with pre-COVID, early COVID (period without elective cases), and late COVID (period with resumed elective cases). Inclusion criteria were cases related to burns. Case types and operative metrics were compared amongst the three time-periods. Compared to the hospital, the burn service had a smaller decrease in volume during early COVID (28.7% vs 50.1%) and exceeded prepandemic volumes during late COVID (+21.8% vs -4.6%). There was a significant increase in excision and grafting cases in early and late COVID periods (P &lt; .0001 and P &lt; .002). There was a significant decrease in laser scar procedures that persisted even during late COVID (P &lt; .0001). The projected and actual lengths of cases significantly increased and persisted into late COVID (P &lt; .01). COVID-19 related operating room closures led to an expected decrease in the number of operative cases. However, there was no significant decline in the number of burn specific cases. The elective cases were largely replaced with excision and grafting cases and this shift has persisted even after elective cases have resumed. This change is also reflected in increased operative times.
Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern
Authors: Wood Dustin A , Richmond Jonathan Q , Escalona Merly , Marimuthu Mohan P A , Nguyen Oanh , Sacco Samuel , Beraut Eric , Westphal Michael , Fisher Robert N , Vandergast Amy G , Toffelmier Erin , Wang Ian J , Shaffer H Bradley 
Published: August 2022

Abstract
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
An unusual case of abdominal compartment syndrome from a massive faecaloma
Authors: Chuang Fred Jui-Ju , Lim Aaron Er-Wynn , Cooper Michelle Louise , Townend Phillip , Parker David James 
Published: August 2022

Abstract
Severe constipation is a frequent presentation but progression into a life-threatening acute compartment syndrome (ACS) is few and far between. This case highlights the typical physiological manifestations of ACS and the immediate benefits of correcting these physiological imbalances through the disimpaction of a massive faecaloma. Furthermore, in adult patients with a history of colonic dysmotility, adult Hirschsprung’s disease should be considered.
Separating the effects of air and soil temperature on silver birch. Part I. Does soil temperature or resource competition determine the timing of root growth?
Authors: Kilpeläinen Jouni , Domisch Timo , Lehto Tarja , Piirainen Sirpa , Silvennoinen Raimo , Repo Tapani 
Published: August 2022

Abstract
The aboveground parts of boreal forest trees mostly grow earlier, and the roots later, in the growing season. We aimed to experimentally test whether the extrinsic driver of soil temperature or the intrinsic driver (resource competition between plant parts) is a more important control for the root and shoot growth of silver birch (Betula pendula Roth) seedlings. Sixteen two-year-old seedlings were grown in controlled environment rooms for two simulated growing seasons (GS1, GS2). In GS1, all the seedlings were acclimatized under the same conditions, but in GS2, the soil temperature treatments were: (i) constant 10 °C (Cool); (ii) constant 18 °C (Warm); (iii) early growing season at 10 °C, switched to 18 °C later (Early Cool Late Warm, ECLW) and (iv) early growing season 18 °C, switched to 10 °C later (Early Warm Late Cool, EWLC). The treatments did not affect growth allocation between shoots and roots. Warm soil benefitted shoot elongation as it slowed down in EWLC and accelerated in ECLW after the soil temperature switch. However, whole-tree biomasses were similar to Cool and the seedlings grew largest in Warm. Phenology was not strongly affected by soil temperature, and root and shoot growth did not usually peak simultaneously. Short root mortality increased strongly in ECLW and decreased in EWLC after the soil temperature switch. Long root longevity was not significantly affected but long root growth ceased earliest in ECLW. Soil warming increased foliar nutrient contents. Growth dynamics were not solely driven by soil temperature, but resource competition also played a significant role. The study showed the importance of soil temperature for fine root dynamics not only through root growth but also via root mortality, as soil warming increased mortality even more than growth. Soil temperature has complex effects on tree and soil functioning, which further affects carbon dynamics in forest ecosystems that have a climate feedback.
A Global Transcriptome and Co-expression Analysis Reveals Robust Host Defense Pathway Reprogramming and Identifies Key Regulators of Early Phases of Cicer-Ascochyta Interactions
Authors: Singh Ritu , Dwivedi Aditi , Singh Yeshveer , Kumar Kamal , Ranjan Aashish , Verma Praveen Kumar 
Published: August 2022

Ascochyta blight (AB) caused by the filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive to date. Here, we investigated the comparative transcriptional dynamics of AB-resistant and -susceptible chickpea genotypes upon A. rabiei infection, to understand the early host defense response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared with a susceptible host. At the early stage (24 h postinoculation [hpi]), mainly cell-wall remodeling and secondary metabolite pathways were highly activated, while differentially expressed genes related to signaling components, such as protein kinases, transcription factors, and hormonal pathways, show a remarkable upsurge at 72 hpi, especially in the resistant genotype. Notably, our data suggest an imperative role of jasmonic acid, ethylene, and abscisic acid signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell-wall remodeling, signal transduction, and phytohormone pathways. Hub genes such as MYB14, PRE6, and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance and susceptibility at early Cicer-Ascochyta interactions but, also, offer a valuable resource for developing AB-resistant chickpea. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
3-Year Outcomes of XEN Implant Compared With Trabeculectomy, With or Without Phacoemulsification for Open Angle Glaucoma
Authors: Marcos-Parra María Teresa , Mendoza-Moreira Angi Lizbeth , Moreno-Castro Lucía , Mateos-Marcos Carlos , Salinas-López Javier Alejandro , Figuerola-García María Belén , González-Alonso Ángela , Pérez-Santonja Juan José 
Published: August 2022

Précis:
Trabeculectomy (TRAB) surgery reduces the intraocular pressure (IOP) more than the XEN45 implant over 3 years. There is no difference in the number of antiglaucoma medications between the 2 procedures. The decision to perform either TRAB or XEN45 implantation must be evaluated on a case-by-case basis, taking into account the high rate of needling of the XEN45.

Purpose:
The aim of this study was to compare the differences between the efficacy and safety of the XEN45 implant and TRAB, either alone or in combination with phacoemulsification (PHACO), in patients with open angle glaucoma (OAG) at 36 months.

Methods:
A retrospective, single-center and comparative study conducted on OAG patients who underwent XEN45 implantation or TRAB from 2016 to 2018. Patients were divided into 4 groups: group 1 (XEN45 alone), group 2 (XEN45+PHACO), group 3 (TRAB alone), and group 4 (TRAB+PHACO). For statistical purposes, groups 1 and 2 were combined (XEN45 implant), whereas groups 3 and 4 were also combined (TRAB surgery). IOP, number of glaucoma medications, and adverse events were evaluated. The main outcome measure was the reduction in IOP at 36 months postoperatively.

Results:
One hundred thirty-four patients (134 eyes; 63 XEN45 and 71 TRAB) were included. The mean (95% confidence interval) IOP reduction at the end of the study follow-up was −6.3 (−11.0 to −1.6 mm Hg, P=0.025, XEN45 alone), −8.9 (−11.0 to −6.8 mm Hg, P<0.001, TRAB alone), −2.5 (−4.5 to −0.4 mm Hg, P=0.019, XEN45+PHACO), and −5.6 (−7.7 to −3.4 mm Hg, P<0.001, TRAB±PHACO). The proportion of patients achieving an IOP≥6 and ≤16 mm Hg without treatment at the end of the 36-month follow-up were 50.8% (32/63) in the XEN45 implant and 49.3% (35/71) in the TRAB surgery group, P=0.863. The mean number of glaucoma medications was significantly reduced in all the study groups. The needling rate was 19% in XEN45 versus 5.6% in the TRAB group (P=0.030), and 2.81% and 36.6% of eyes in the TRAB group presented anterior chamber flattening and hyphema, respectively.

Conclusions:
TRAB surgery lowered IOP significantly more than XEN45 implant with or without phacoemulsification over 3 years and had a significantly lower need for additional needling surgery. Both procedures reduced glaucoma medications to a similar rate. These findings are relevant to the informed consent process and patient decisions for one procedure over the other.
Health effects of androgen abuse: a review of the HAARLEM study
Authors: Smit Diederik L. , Bond Peter , de Ronde Willem 
Published: August 2022

Purpose of review
Data on the health effects of androgen abuse are mainly derived from lower level evidence, such as case series and cross-sectional studies. In the last few years a relatively large and prospective cohort initiative, the HAARLEM (health risks of anabolic androgenic steroid use by male amateur athletes) study, made an important contribution to current knowledge.

Recent findings
The HAARLEM study showed that all androgen abusers experience positive and negative effects, such as an increase in strength and acne and gynecomastia, respectively. Effects are generally reversible and acute life-threatening toxicity is rare. There is a distinct but limited impact on liver and kidney function. Gonadal function is disrupted but resumes normally after abuse is discontinued in the majority of athletes. The negative impact of androgens on cardiovascular parameters, such as blood pressure, hematocrit and lipid metabolism, as well as cardiac structure and function, seems to be the mechanism for premature atherosclerosis and cardiomyopathy, respectively, in long-term users.

Summary
It is beyond dispute that androgen abuse is harmful and much of the short-term toxicity is well documented. To prevent the long-term health hazards, there should be ample focus on preventive measures, both primary and secondary, and effective harm reduction strategies should be developed.
Assessing cardiovascular disease: looking beyond cholesterol
Authors: Kendrick Malcolm 
Published: August 2022

Purpose of review
The low-density lipoprotein (LDL)-cholesterol level is a weak predictor of developing cardiovascular (CV) disease and can only explain a small proportion of CV risk. It is not used to determine CV risk on either the atherosclerotic cardiovascular disease (ASCVD) calculator in the United States, or the Qrisk3 in the UK.
A study in JAMA in 2022 suggested that ‘the absolute benefits of statins are modest and may not be strongly mediated through the degree of LDL reduction’. Perhaps it is time to look beyond cholesterol to a different causal model – the ‘thrombogenic’ model of ASCVD.

Recent findings
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) pandemic demonstrated that infectious agents damage the endothelium and the glycocalyx – the glycoprotein layer protecting underlying endothelial cells. There are numerous other conditions leading to this kind of damage, which can trigger thrombus formation, causing strokes and myocardial infarctions.
Although these are acute events, they highlight a mechanism for the development of ASCVD which centres on endothelial damage and thrombus formation as both the primary causal mechanism for acute events, and the driver behind progression towards atherosclerotic plaque development.

Summary
The cholesterol hypothesis, that a raised LDL is directly causal for ASCVD, does not adequately explain cardiovascular risk in individuals, or populations. An alternative ‘thrombogenic’ hypothesis is proposed as a more valid causal model.
Flexible use of contact calls in a species with high fission–fusion dynamics
Authors: Briseño-Jaramillo Margarita , Sosa-López José Roberto , Ramos-Fernández Gabriel , Lemasson Alban 
Published: August 2022

The ‘social complexity hypothesis' posits that complex social systems (which entail high uncertainty) require complex communicative systems (with high vocal flexibility). In species with fission–fusion dynamics, where the fluid composition of temporary subgroups increases the uncertainty with which group members must manage their social relationships, vocal communication must be particularly flexible. This study assessed whether contact call rates vary with caller and audience characteristics in free-living spider monkeys, as well as with fission and fusion events. Adult females and immature individuals called more when in small audience settings, while audience size did not influence adult males. Adults called more when in the presence of the opposite sex, whereas immatures vocalized more in subgroups composed only by females. Females also called more when with their mature sons. We found higher call rates in periods during which fission and fusion events took place than in periods with more stable compositions and when the composition after a fission or fusion event changed from one sex to two sexes. A flexible use of contact calls allows individuals to identify themselves when they join others, particularly if they are members of the opposite sex. This socio-spatial cohesion function reduces the uncertainty about subgroup composition.This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
An open-access T-BAS phylogeny for EmergingPhytophthoraspecies
Authors: Coomber Allison , Saville Amanda , Carbone Ignazio , Ristaino Jean Beagle 
Published: August 2022

AbstractPhytophthoraspecies cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1875, it has expanded to comprise over 190 formally described species. There is a need for an open access bioinformatic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification ofPhytophthoraspecies. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genusPhytophthorausing sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood method. A search engine was also developed to identify genotypes ofP. infestansbased on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of allPhytophthoraspecies. Critically, this resource can be updated in real-time to keep pace with new species descriptions. The tool contains metadata such as clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the globalPhytophthoracommunity to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community ofPhytophthoraresearchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for diverse populations of pathogens.
Expansive growths with uniaxial gradients can explain formation of oblong diversity observed in two-dimensional leaf shapes
Authors: Nakamasu Akiko M. 
Published: August 2022

AbstractRegulation of positional information in fields with different sizes are known as scaling in the area of morphogenesis, and enable integrated and robust developmental processes. Although it is known that interpretation of such scaled patterns leads to formations of relative shapes, the same positional information brings about diversities in morphogenesis.In this research, a boundary of a two-dimensional shape was constructed by propagating points and segments connecting them for a description of a growing form. Cell expansion “with” or “without” cell proliferation were implemented using different simple algorithms, as “additive growth” and “expansive growth”, respectively. When the different types of growth algorithm with a biased restriction were calculated, the additive growth maintained a relative shape corresponding to the gradients with different lengths. However, diverse shapes were generated by the gradients in the cases of expansive growth and its combinations even with negate effects by additive growth. As an operative example of this attempt, leaf shapes with smooth margins were calculated using a combination of these growth algorithms.Finally, we concluded that different algorithms brought different responses against the simple positional information, i.e., additive growth always governed by it or expansive growth can escape it. It was predicted theoretically that an expansive growth has a capacity to become a generator of diversity at least in leaf morphogenesis.Summary statementExplanation of different responses against single positional information by different algorithms for two types of growth modes.
ATG5- and ATG7-mediated autophagy regulates pollen tube guidance and male fertility in Arabidopsis thaliana
Authors: Yan He , Du Xiaojuan , Yang Mingkang , Li Nianle , Li Xuequan , Ni Zailue , Huang Wei , Wu Hong , Zhao Lifeng , Wang Hao 
Published: August 2022

AbstractAutophagy functions as a crucial cellular scavenger by targeting cytoplasmic cargo to specific lysosome/vacuole for degradation. Autophagy-related (ATG) core proteins including ATG5 and ATG7 are evolutionarily conserved factors that are spatiotemporally orchestrated to regulate multiple processes of autophagy in yeast, mammalian and plant cells. However, autophagy is believed to be functionally dispensable in Arabidopsis thaliana since severe defects during plant growth, development and reproduction have not been observed in most of the ATG loss-of-function mutants, including atg5 and atg7, under standard cultivation conditions. In this study, we report that autophagy does in fact play roles in regulating pollen tube growth guidance and male fertility in Arabidopsis thaliana. A detailed re-assessment of atg5 and atg7 mutants revealed greatly reduced autophagy activity in germinated pollens and the seed formation within siliques is partially abolished. Next, we demonstrated that both the pollen germination ratio and pollen tube length of the mutants decreased at the beginning of germination by time-lapse tracking of pollen germination in vitro and in vivo. Additionally, we observed occurrences of pollen tube twisting and stacking during their growth towards the ovules. Finally, we found abnormal pollen grains containing only a single sperm cell or an undivided generative nucleus. Collectively, these results indicate that ATG5- and ATG7-mediated autophagy is functionally involved in regulating pollen germination, tube growth guidance and sperm cell development in Arabidopsis thaliana.