bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Review of Microsurgical Pedicle Lengthening in Free Tissue Transfer
Authors: Soto Edgar , Peacock Paxton W. , Clark Ashlynn R. , King Timothy W. , de la Torre Jorge I. , Patcha Prasanth , Fix R. Jobe , Myers René P. 
Published: June 2023

Introduction
Traumatic injuries that require free tissue flaps for reconstruction may require vascular pedicle extension between the flap and recipient vessels to form a clear anastomosis. Currently, a variety of techniques are used, each with their own potential benefits and harms. In addition, reports in the literature conflict on the reliability of pedicle extensions of vessels in free flap (FF) surgery. The objective of this study is to systematically assess the available literature about outcomes of pedicle extensions in FF reconstruction.

Methods
A comprehensive search was performed for relevant studies published up to January 2020. Study quality was assessed using the Cochrane Collaboration risk of bias assessment tool and a set of predetermined parameters was extracted by 2 investigators independently for further analysis. The literature review yielded 49 studies investigating pedicled extension of FF. Studies meeting inclusion criteria underwent data extraction focusing on demographics, conduit type, microsurgical technique, and postoperative outcomes.

Results
The search yielded 22 retrospective studies totaling 855 procedures from 2007 to 2018 in which 159 complications (17.1%) were reported in patients aged between 39 and 78 years. Overall heterogeneity of articles included in this study was high. Free flap failure and thrombosis were the 2 most prevalent major complications noted: vein graft extension technique had the highest rate of flap failure (11%) in comparison with the arterial graft (9%) and arteriovenous loops (8%). Arteriovenous loops had a rate of thrombosis of 5% versus 6% in arterial grafts and 8% in venous grafts. Bone flaps maintained the highest overall complication rates per tissue type at 21%. The overall success rate of pedicle extensions in FFs was 91%. Arteriovenous loop extension resulted in a 63% decrease in the odds of vascular thrombosis and a 27% decrease in the odds of FF failure when compared with venous graft extensions (P < 0.05). Arterial graft extension resulted in a 25% decrease in the odds of venous thrombosis and a 19% decrease in the odds of FF failure when compared with venous graft extensions (P < 0.05).

Conclusions
This systematic review strongly suggests that pedicle extensions of the FF in a high-risk complex setting are a practical and effective option. There may be a benefit to using arterial versus venous conduits, although further examination is warranted given the small number of reconstructions reported in the literature.
Waitlist and Transplant Outcomes in Organ Donation After Circulatory Death
Authors: Kwon Jennie H. , Blanding Walker M. , Shorbaji Khaled , Scalea Joseph R. , Gibney Barry C. , Baliga Prabhakar K. , Kilic Arman 
Published: June 2023

Objectives:
To summarize waitlist and transplant outcomes in kidney, liver, lung, and heart transplantation using organ donation after circulatory death (DCD).

Background:
DCD has expanded the donor pool for solid organ transplantation, most recently for heart transplantation.

Methods:
The United Network for Organ Sharing registry was used to identify adult transplant candidates and recipients in the most recent allocation policy eras for kidney, liver, lung, and heart transplantation. Transplant candidates and recipients were grouped by acceptance criteria for DCD versus brain-dead donors [donation after brain death (DBD)] only and DCD versus DBD transplant, respectively. Propensity matching and competing-risks regression was used to model waitlist outcomes. Survival was modeled using propensity matching and Kaplan-Meier and Cox regression analysis.

Results:
DCD transplant volumes have increased significantly across all organs. Liver candidates listed for DCD organs were more likely to undergo transplantation compared with propensity-matched candidates listed for DBD only, and heart and liver transplant candidates listed for DCD were less likely to experience death or clinical deterioration requiring waitlist inactivation. Propensity-matched DCD recipients demonstrated an increased mortality risk up to 5 years after liver and kidney transplantation and up to 3 years after lung transplantation compared with DBD. There was no difference in 1-year mortality between DCD and DBD heart transplantation.

Conclusions:
DCD continues to expand access to transplantation and improves waitlist outcomes for liver and heart transplant candidates. Despite an increased risk for mortality with DCD kidney, liver, and lung transplantation, survival with DCD transplant remains acceptable.
Patient-reported Adverse Events During Neoadjuvant Therapy in a Phase 2 Borderline Resectable Pancreatic Cancer Clinical Trial (Alliance A021501)
Authors: Snyder Rebecca A. , Dueck Amylou C. , Fruth Briant , Shi Qian , Hubbard Joleen M. , Herman Joseph M. , O’Reilly Eileen M. , Katz Matthew H.G. 
Published: June 2023

Objective:
We sought to evaluate symptomatic adverse event (AE) rates among patients with pancreatic cancer receiving neoadjuvant therapy on clinical trial (A021501) using the Patient-Reported Outcomes Common Terminology Criteria for Adverse Events (PRO-CTCAE).

Background:
To date, pancreatic cancer clinical trials have measured AEs using standard physician reporting [Common Terminology Criteria for Adverse Events (CTCAE)]. Patient-reported symptomatic AEs have been incompletely characterized.

Methods:
A021501 (December 31, 2016–January 1, 2019) randomized patients with borderline resectable pancreatic ductal adenocarcinoma to 8 doses of mFOLFIRINOX (Arm 1) or 7 doses of mFOLFIRINOX+hypofractionated radiotherapy (Arm 2), followed by pancreatectomy and adjuvant FOLFOX6. Patients completed PRO-CTCAE assessments at baseline, on day 1 of each chemotherapy cycle, and daily during radiotherapy.

Results:
Of 126 patients, 96 (76%) initiated treatment and completed a baseline plus at least 1 postbaseline PRO-CTCAE assessment. Diarrhea and fatigue were the only symptomatic grade 3 or higher AEs identified in at least 10% of patients using CTCAE. At least 10% of all patients reported an adjusted PRO-CTCAE composite grade 3 AE during neoadjuvant treatment for 10 of 15 items: anxiety (10%), bloating of abdomen (16%), decreased appetite (18%), diarrhea (13%), dry mouth (21%), fatigue (36%), nausea (18%), generalized pain (16%), abdominal pain (21%), and problems tasting (32%). Decreased appetite was higher in Arm 2 than in Arm 1 (P=0.0497); no other differences between study arms were observed.

Conclusion:
Symptomatic AEs during neoadjuvant therapy were common and were reported more frequently by patients using PRO-CTCAE than were recorded by clinicians using standard CTCAE.
Screening, prevention, and management of patients with poststroke depression in a tertiary hospital in China: a best practice implementation project
Authors: Tan Jing , Brancatisano Olivia , Cadilhac Dominique A. , Deng Bo , Wu Yanni , Li Yan , Liu Ning 
Published: June 2023

ABSTRACT

Introduction:
Poststroke depression (PSD) is common but insufficiently addressed by health professionals, and management is not always evidence-based.

Objectives:
This evidence implementation project aimed to improve adherence to evidence-based practice for screening, prevention, and management of patients with PSD in the neurology ward of the Fifth Affiliated Hospital of Zunyi Medical University, China.

Methods:
This project was based on the JBI methodological approach and was conducted in three phases, from January to June 2021: a baseline audit, implementation of strategies, and a follow-up audit. We utilized the JBI Practical Application of Clinical Evidence System software and the Getting Research into Practice tools. Fourteen nurses, 162 stroke patients, and their caregivers participated in this study.

Results:
The results of the baseline audit showed that compliance with evidence-based practice was poor, with 3/6 criteria showing 0% adherence and the other three audit criteria showing 5.7, 10.3, and 49.4% adherence, respectively. Through feedback to nurses regarding the baseline audit results, the project team identified five barriers and adopted a battery of strategies to overcome these barriers. The follow-up audit revealed significantly enhanced outcomes across all the best practice criteria, and the compliance of each criterion reached at least 80%.

Conclusion:
The implementation program designed to screen, prevent, and manage PSD in a tertiary hospital in China improved nurses’ knowledge and compliance with evidence-based management of PSD. Further testing of this program in more hospitals is needed.
A grand unified theory for the unification of physics, life, information and cognition (mind)
Authors: Swenson Rod 
Published: June 2023

The modern scientific world view was built on the incommensurability between cognition (mind) and physics (matter) and later life and physics (the autonomy of biology). Fuelled by Boltzmann's view of the second law of thermodynamics as a ‘law of disorder’, the idea of ‘two opposing rivers’, the river of physics ‘flowing down’ to disorder and the river of life and mind ‘flowing up’ to higher states of order became a cornerstone of contemporary thinking. The deleterious result of this paradigmatic separation of physics, life and mind has been to considerably incapacitate each by bracketing many of the deepest problems of science, including the very nature of life itself and its cognitive capabilities, outside the theoretical reach of contemporary science. An expanded view of physics, notably the addition of the fourth law of thermodynamics (LMEP), or the law of maximum entropy production, coupled with first law time-translation symmetry, and the self-referencing circularity of the relational ontology of autocatakinetic systems, provides the basis for a grand unified theory unifying physics, life, information and cognition (mind). This dissolves the dysfunctional myth of the two rivers, and solves the previously insoluble problems at the foundations of modern science associated with it.
This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)’.
Philosophy of thermodynamics
Authors: Annila Arto 
Published: June 2023

Thermodynamics is regarded as a universal but not foundational theory because its laws for macroscopic quantities have not been derived from microscopic entities. Thus, to root thermodynamics into the fundamental substance, atomism is revived, thinking that the light quantum is the indivisible and permanent element. Assuming the same basic building blocks constitute everything, the state of any system can be quantified by entropy, the logarithmic probability measure multiplied by Boltzmann’s constant. Then, the change in entropy expresses the system’s evolution toward thermodynamic balance with its surroundings. These natural processes consuming free energy in the least time accumulate sigmoidally, resulting in skewed distributions found throughout nature. In this way, thermodynamics makes sense of phenomena across disciplines and provides a holistic worldview to address questions such as what the world is, how we know about it, what is the meaning of life and how we should live.
This article is part of the theme issue ‘’Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)’.
The principle underlying all evolution, biological, geophysical, social and technological
Authors: Bejan Adrian 
Published: June 2023

This article addresses the main research areas identified in the call for contributions to this special issue. With examples from published articles and books, the present article shows that all the identified areas are already covered by the universal principle underlying all evolution: the constructal law (1996), i.e. the physics law of design evolution in nature (free morphing, flowing, moving systems). The universal principle of evolution belongs in thermodynamics because thermodynamics is a universal science and evolution is a universal phenomenon. The principle unites the natural sciences with the social sciences, and the living with the non-living. It unifies the world of science and its languages (energy, economy, evolution, sustainability, etc.), and brings together the natural and artificial flow architectures, the human made and the not human made. The principle establishes firmly in physics the reality that humans are part of nature. With the principle, physics extends its coverage over phenomena that were previously considered out of reach: social organization, economics and human perceptions. Such phenomena are physical, i.e. facts. The entire world depends on the science of useful things, and benefits greatly from a physics discipline with freedom, life, wealth, time, beauty and future.
This article is part of the theme issue 'Thermodynamics 2.0: bridging the natural and social sciences (Part 1)'.
EFFECT OF DIETARY CALCIUM ON INCIDENCE OF CALCIUM STONES AND URINARY PARAMETERS: A SYSTEMATIC REVIEW
Authors: Desai Dev , Sahni Tanvi , Andharia Dev Umangbhai , Raval Dwija 
Published: June 2023

ABSTRACTIntroductionRenal stone is a fairly common presentation and the pain is unbearable. Some patients have tendency that stones are frequently formed and management of that s necessary as removal of stone is nt always that simple and can lead to many complications.Aims and ObjectivesTo perform a systematic review and meta-analysis to investigate the effect of dietary calcium on the prevention of calcium stones.MethodologyPubMed, google scholar and Cochrane Library databases were searched for studies. The search strategy and study selection process was conducted by following the PRISMA statement. 16 articles were identified after meeting the inclusion criteria.ResultsOur results showed that with high calcium advice, occurrence of stone formation decreases (RR=0.82, CI95=0.37-1.82, p=0.63). Comparing levels of Urinary caclium with advice of high calcium diet showed increased excretion (SMD=1.99), but decreased excretion with low calcium diet (SMD = -0.43) and Normal calcium diet (SMD = -1.35). An almost no difference can be seen in Urinary oxalate with high calcium (SMD = 0.00), low calcium (SMD = 0.02), Normal Calcium (SMD = -0.052). Results showed that Urinary Urate levels decreased with all types of diet mainly with High calcium diet (SMD = -0.33), then Low calcium diet (SMD = -0.28)and then normal calcium (SMD = -0.22). Urinary Volume was increased with all dietary advice, the most with low calcium diet(SMD = 216.37), then normal calcium diet (SMD = 206.81) and last high calcium diet (SMD = 20.00).Conclusionur study shows high calcium diet decreases the occurrence of stones compared to normal calcium and low calcium diet.
The public health impact of Paxlovid COVID-19 treatment in the United States
Authors: Bai Yuan , Du Zhanwei , Wang Lin , Lau Eric H. Y. , Fung Isaac Chun-Hai , Holme Petter , Cowling Benjamin J. , Galvani Alison P. , Krug Robert M. , Meyers Lauren Ancel 
Published: June 2023

AbstractThe antiviral drug Paxlovid has been shown to rapidly reduce viral load. Coupled with vaccination, timely administration of safe and effective antivirals could provide a path towards managing COVID-19 without restrictive non-pharmaceutical measures. Here, we estimate the population-level impacts of expanding treatment with Paxlovid in the US using a multi-scale mathematical model of SARS-CoV-2 transmission that incorporates the within-host viral load dynamics of the Omicron variant. We find that, under a low transmission scenario (Re∼ 1.2) treating 20% of symptomatic cases would be life and cost saving, leading to an estimated 0.26 (95% CrI: 0.03, 0.59) million hospitalizations averted, 30.61 (95% CrI: 1.69, 71.15) thousand deaths averted, and US$52.16 (95% CrI: 2.62, 122.63) billion reduction in health- and treatment-related costs. Rapid and broad use of the antiviral Paxlovid could substantially reduce COVID-19 morbidity and mortality, while averting socioeconomic hardship.Article Summary LineMass treatment of symptomatic COVID-19 cases with antivirals that rapidly arrest SARS-CoV-2 replication would substantially reduce the spread and burden of the pandemic.
Neurometabolite changes in response to antidepressant medication: a systematic review of1H-MRS findings
Authors: Boucherie Daphne E. , Reneman Liesbeth , Ruhé Henricus G. , Schrantee Anouk 
Published: June 2023

ABSTRACTSelective serotonin reuptake inhibitors (SSRIs), serotonin and noradrenaline reuptake inhibitors (SNRIs), and (es-)ketamine are used to treat major depressive disorder (MDD). These different types of medication may involve common neural pathways related to glutamatergic and GABAergic neurotransmitter systems, both of which have been implicated in MDD pathology. We conducted a systematic review of pharmacological1H-MRS studies in healthy volunteers and MDD patients to explore the potential impact of these medications on glutamatergic and GABAergic systems. Studies on SSRIs and SNRIs were highly variable, generally underpowered, and yielded no consistent findings across brain regions or specific populations. Although studies on (es-)ketamine were also highly variable, some demonstrated an increase in glutamate levels in the anterior cingulate cortex in a time-dependent manner after administration. Our findings highlight the need for standardized study and acquisition protocols. Additionally, measuring metabolites dynamically over time or combining1H-MRS with whole brain functional imaging techniques could provide valuable insights into the effects of these medications on glutamate and GABAergic neurometabolism.
Multiple imputation of missing data under missing at random: including a collider as an auxiliary variable in the imputation model can induce bias
Authors: Curnow Elinor , Tilling Kate , Heron Jon E , Cornish Rosie P , Carpenter James R 
Published: June 2023

AbstractEpidemiological studies often have missing data, which are commonly handled by multiple imputation (MI). In MI, in addition to those required for the substantive analysis, imputation models often include other variables (“auxiliary variables”). Auxiliary variables that predict the partially observed variables can reduce the standard error (SE) of the MI estimator and, if they also predict the probability that data are missing, reduce bias due to data being missing not at random. However, guidance for choosing auxiliary variables is lacking. We examine the consequences of a poorly-chosen auxiliary variable: if it shares a common cause with the partially observed variableandthe probability that it is missing (i.e. it is a “collider”), its inclusion can induce bias in the MI estimator and may increase SE. We quantify, both algebraically and by simulation, the magnitude of bias and SE when either the exposure or outcome are incomplete. When the substantive analysis outcome is partially observed, the bias can be substantial, relative to the magnitude of the exposure coefficient. In settings in which complete records analysis is valid, the bias is smaller when the exposure is partially observed. However, bias can be larger if the outcome also causes missingness in the exposure. When using MI, it is important to examine, through a combination of data exploration and considering plausible casual diagrams and missingness mechanisms, whether potential auxiliary variables are colliders.Contribution to the field statementIn multiple imputation (MI), in addition to those required for the substantive analysis, imputation models often include other variables (“auxiliary variables”). Auxiliary variables that predict the partially observed variables can reduce the standard error (SE) of the MI estimator and, if they also predict the probability that data are missing, reduce bias due to data being missing not at random. We examine the consequences of a poorly-chosen auxiliary variable: if it shares a common cause with the partially observed variableandthe probability that it is missing (i.e. it is a “collider”), its inclusion can induce bias in the MI estimator and may increase SE. We demonstrate that when the substantive analysis outcome is partially observed, the bias can be substantial, relative to the magnitude of the exposure coefficient. In settings in which complete records analysis is valid, the bias is smaller when the exposure is partially observed. However, bias can be larger if the outcome also causes missingness in the exposure. We recommmend a combination of data exploration and consideration of plausible casual diagrams and missingness mechanisms to examine whether potential auxiliary variables are colliders.
Large language models are universal biomedical simulators
Authors: Schaefer Moritz , Reichl Stephan , ter Horst Rob , Nicolas Adele M. , Krausgruber Thomas , Piras Francesco , Stepper Peter , Bock Christoph , Samwald Matthias 
Published: June 2023

AbstractComputational simulation of biological processes can be a valuable tool in accelerating biomedical research, but usually requires extensive domain knowledge and manual adaptation. Recently, large language models (LLMs) such as GPT-4 have proven surprisingly successful for a wide range of tasks by generating human language at a very large scale. Here we explore the potential of leveraging LLMs as simulators of biological systems. We establish proof-of-concept of a text-based simulator, SimulateGPT, that uses LLM reasoning. We demonstrate good prediction performance for various biomedical applications, without requiring explicit domain knowledge or manual tuning. LLMs thus enable a new class of versatile and broadly applicable biological simulators. This text-based simulation paradigm is well-suited for modeling and understanding complex living systems that are difficult to describe with physics-based first-principles simulation, but for which extensive knowledge and context is available as written text.
Diffusion model of delipidation in biological sample clearing
Authors: Han Jinglu , Liu Xinyi , Hou Xiaoxiao , Zhong Yuejia , Chen Zhiqiang , Yang Zhenyi , Jiang Tianzi 
Published: June 2023

AbstractBiological sample clearing techniques are a potent tool for three-dimensional biological imaging, among which delipidation is an essential step in achieving high-quality biological sample transparency. Detergents and organic solvents can both be used for lipids removal. The former has been extensively investigated in biological sample clearing, while the delipidation process based on organic solvents remains to be further elucidated. Recently, organic solvents also served as a delipidation reagent in aqueous-based clearing methods and exhibited very fast clearing speed. To explain the high efficiency of organic solvents, we described the delipidation process of both detergents and organic solvents with a simple diffusion model, we proposed a possible mechanism of the delipidation process of water-miscible polar organic solvents based on the clearing results of brain samples. Both our results and model revealed that polar or non-polar organic solvents with a certain molecular structure could achieve a much faster clearing speed than detergents which could be a guide for establishing a rapid clearing protocol for biological samples with large volumes.