bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing
Authors: Taylor Alysha S , Barros Dinis , Gobet Nastassia , Schuepbach Thierry , McAllister Branduff , Aeschbach Lorene , Randall Emma L , Trofimenko Evgeniya , Heuchan Eleanor R , Barszcz Paula , Ciosi Marc , Morgan Joanne , Hafford-Tear Nathaniel J , Davidson Alice E , Massey Thomas H , Monckton Darren G , Jones Lesley , network REGISTRY Investigators of the European Huntington’s disease , Xenarios Ioannis , Dion Vincent 
Published: December 2022

AbstractTargeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington’s disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington’s disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and in the development of novel therapies.
Relationship Between a State-Directed Lockdown on Non-COVID-19–related ICU Admissions and Mortality in a Multicenter Colorado Healthcare System
Authors: Park Bryan D. , Kannappan Arun , Rizzo Alicia N. , Jin Ying , Peterson Ryan A. , Burnham Ellen , Moss Marc , Jolley Sarah 
Published: December 2022

OBJECTIVES:
Colorado issued a month long statewide lockdown on March 26, 2020, during the initial surge of the COVID-19 pandemic. The impact of this mandate on non–COVID-19 ICU admission rates and outcomes is unclear.

DESIGN:
We performed a retrospective analysis of all medical ICU admissions in the University of Colorado Health System in four predefined periods: 1) prepandemic (2 mo prior to lockdown period 1); 2) mandated lockdown from March 26 to April 26, 2020 (period 2); 3) between surges (period 3); and 4) nonmandated lockdown surge (between November 1, 2020, and March 31, 2021, period 4).

SETTING:
Nonsurgical ICU admissions at the University of Colorado Health Systems, including 10 hospitals throughout Colorado.

SUBJECTS:
All ICU admissions in four predefined time periods.

MEASUREMENTS AND MAIN RESULTS:
We included 13,787 patients who were admitted during the four study periods. The 28-day mortality rates for non–COVID-19 ICU admissions following index ICU admission were 13.6%, 18.0%, 13.5%, and 16.0% across periods 1–4, respectively. However, the increased odds in non–COVID-19 ICU mortality during the mandated lockdown period relative to prepandemic 1 (odds ratio [OR], 1.39; 95% CI, 1.11–1.72; p = 0.0.04) was attenuated and nonsignificant after adjustment for demographics, comorbidities, diagnosis flags, and severity (OR, 1.15; 95% CI, 0.89–1.48; p = 0.27). Similar results were found in time-to-event analyses. The most common diagnosis in each time period was acute respiratory failure (ARF), and we found it to have increased during lockdown (p < 0.001), whereas sepsis admissions increased during and decreased after lockdown (p = 0.004). Admissions for alcohol withdrawal syndrome (AWS) increased during lockdown and 6 months afterwards (p = 0.005).

CONCLUSIONS:
For non-COVID-19–related ICU admissions, mortality rate was similar before, during, and after Colorado’s month long lockdown after confounder adjustment, including typical ICU admission flags. Primary admission diagnoses shifted throughout the predefined study periods with more admissions for severe critical diagnoses (i.e., ARF, sepsis, AWS) occurring during the mandated lockdown and nonmandated lockdown periods compared with the prepandemic and between surge period. This would suggest that the perceived increase in mortality during the lockdown for non–COVID-19 ICU admissions may be related to a shift inpatient demographics.
Early Hyperchloremia and Outcomes After Severe Traumatic Brain Injury: Analysis of Resuscitation Outcomes Consortium Hypertonic Saline Trial
Authors: Qureshi Adnan I. , Ma Xiaoyu , Huang Wei , Nunna Ravi S. , Gomez Francisco , Malhotra Kunal , Arora Niraj , Chandrasekaran Premkumar N. , Siddiq Farhan , Gomez Camilo R. , Suarez Jose I. 
Published: December 2022

BACKGROUND/OBJECTIVES:
To investigate the effect of the occurrence of early hyperchloremia on death or severe disability at 180 days in patients with severe traumatic brain injury (TBI).

DESIGN:
Post hoc analysis of Resuscitation Outcomes Consortium Hypertonic Saline (ROC HS)-TBI trial.

SETTING:
A total of 114 North American emergency medical services agencies in the ROC.

PATIENTS:
A total of 991 patients with severe TBI and Glasgow Coma Scale score of less than or equal to 8.

INTERVENTIONS:
Prehospital resuscitation with single IV dose (250 cc) of 7.5% saline in 6% dextran-70, 7.5% saline (no dextran), or crystalloid.

MEASUREMENTS AND MAIN RESULTS:
Patients with increased serum chloride concentrations (110 mmol/L or greater) 24 hours after randomization were identified. Hyperchloremia was graded into one or greater than or equal to 2 occurrences in the first 24 hours. Logistic regression analyses were performed to determine the effects of hyperchloremia on: 1) death or severe disability at 180 days and 2) death within 180 days after adjusting for confounders. Compared with patients without hyperchloremia, patients with greater than or equal to 2 occurrences of hyperchloremia had significantly higher odds of death or severe disability at 180 days (odds ratio [OR], 1.81; 95% CI, 1.19–2.75) and death within 180 days (OR, 1.89; 95% CI, 1.14–3.08) after adjustment for confounders. However, the total volume of fluids administered during the first 24 hours was an independent predictor of death within 180 days; therefore, after adding an interaction term between the total volume of fluids administered during the first 24 hours and greater than or equal to 2 occurrences of hyperchloremia, patients with greater than or equal to 2 occurrences of hyperchloremia had significantly higher odds of death within 180 days (OR, 2.35; 95% CI, 1.21–4.61 d) but not of composite outcome of death or severe disability at 180 days.

CONCLUSIONS:
After modifying for the effect of the total volume of fluids administered during the first 24 hours, multiple occurrences of hyperchloremia in the first 24 hours were associated with higher odds of death within 180 days in patients with severe TBI.
Piloting Group-Based Behavioral Activation Therapy for Families of Deceased COVID-19 Patients
Authors: England Ashley Eaton , Lietzau Stephanie , Vu James , Hebert Charles , Banayan David , Greenberg Jared A. , Gerhart James 
Published: December 2022

BACKGROUND:
Surrogate decision-making is a stressful process for many family members of critically ill patients. The COVID-19 pandemic may have amplified the risk for anxiety, depression, and posttraumatic stress disorder (PTSD) symptoms in ICU surrogates.

OBJECTIVES:
This study piloted an online group-based behavioral intervention with family members of deceased COVID-19 patients. Participant engagement, perceptions, and responses related to the intervention were assessed.

DESIGN:
A single-arm pilot study was conducted with bereaved families. Quantitative analysis of measures of anxiety, depression, and PTSD symptoms was conducted with mixed models. Qualitative data were analyzed to identify themes in surrogates’ experiences with the intervention.

SETTING:
Participants were recruited from ICUs at a tertiary academic medical center. Participants completed the intervention, measures, and interviews online.

SUBJECTS:
Participants were family members of patients who died from COVID-19.

INTERVENTIONS:
The intervention involved six online group-based behavioral activation sessions. Sessions covered topics pertinent to grieving and engagement in personally meaningful activities.

MEASUREMENTS AND MAIN RESULTS:
Semi-structured interviews explored participants’ experiences with the intervention. Surrogates also completed measures of anxiety, depression, and PTSD symptoms before and after the intervention. Nineteen of 26 participants (73.1%) completed the study. Thematic analysis suggested that surrogates found the group helpful for overcoming perceived isolation, receiving validation, and developing coping skills. Significant pre-to-post reductions were observed in symptoms of Hospital and Anxiety Disorder Scale (HADS) anxiety (pre-mean = 9.27, sd = 5.30 vs post-mean = 6.80, sd = 4.16; p = 0.0271), HADS depression (pre-mean =6 .65, sd = 4.58 vs post- mean = 4.89, sd = 3.40; p = 0.0436), and Impact of Events Scale-Revised PTSD (pre-mean = 36.86, sd = 16.97 vs post-mean = 24.14, sd = 13.49; p = 0.0008).

LIMITATIONS:
This was a preliminary study based on qualitative and self-report measures. Future studies should include a control group.

CONCLUSIONS:
Online group-based behavioral activation therapy appears to be a potentially useful intervention for family members of ICU patients who died from COVID-19.
COVID-19 Caregiving Strategies, Quality of Life, and Stress Among Faith Community Nurses and Faith Leaders in Appalachia
Authors: Smothers Angel , Morrissey Elizabeth , Melnick Helen , Beaver Molly , Wang Kesheng , Piamjariyakul Ubolrat 
Published: December 2022

ABSTRACT:
Faith community nurses (FCNs), pastors, and priests faced many challenges from the COVID-19 pandemic, serving as frontline sources of support for congregants. The aim of this study was to identify the most common care strategies used during the COVID-19 pandemic and examine professional quality of life, perceived stress, and associated factors in faith leaders and FCNs in rural Appalachia. Using a cross-sectional, descriptive survey design, high compassion satisfaction was reported along with compassion fatigue as caregiving moved to virtual platforms, suggesting the need for greater support.
A Faith-Based Intervention to Address Social Isolation and Loneliness in Older Adults
Authors: Blevins Don'L 
Published: December 2022

ABSTRACT:
The goal of this quality improvement project was to determine if virtually offered faith-based resources for socially isolated older adults could reduce loneliness and improve quality of life. A nurse-developed program of virtual spiritual and religious interventions, including mindfulness, prayer, Scripture meditation, gratitude practices, and online church services, was offered by local ministers to older adults at risk of social isolation or loneliness. A sample of 16 adults over age 55 from local communities participated in the 12-week intervention and follow-up. The intervention resulted in a significant decrease in perception of social loneliness and improved physical health quality of life.
The important primary care role of neonatal nurse practitioners in the neonatal intensive care unit
Authors: Etten Kristen , Hoffman Jacqui , Wallman Carol , Bellflower Bobby 
Published: December 2022

ABSTRACT
Neonatal nurse practitioners (NNPs) are recognized as acute care providers but are actually both acute and primary care providers via education and practice. Neonatal nurse practitioners provide primary care such as anticipatory guidance, care and follow-up of technologically dependent infants, and discharge planning. Numerous interventions and care in the neonatal intensive care unit (NICU) fall under the umbrella of health promotion, an aspect of primary care. In addition, NNPs must also be able to recognize, diagnose, and manage myriad common pediatric illnesses. There is a paucity of data to evaluate how NNP programs are meeting the National Association of Neonatal Nurses educational standards on this topic. A REDCap survey was sent to 31 NNP program directors, with a 100% response rate. All programs provide content addressing primary care management in their curriculum. National recognition of the primary care role, in addition to the acute care role that NNPs practice, should increase opportunities for clinical placement sites, employment opportunities, and grant funding. This article aims to demonstrate both the educational preparation and the delivery of primary care that NNPs provide in the NICU and other areas of practice.
Oral omeprazole and diclofenac intake is associated with increased faecal calprotectin levels: a randomised open-label clinical trial
Authors: Rendek Zlatica , Falk Magnus , Grodzinsky Ewa , Kechagias Stergios , Hjortswang Henrik 
Published: December 2022

Background and aim
Nonsteroidal anti-inflammatory drugs and proton pump inhibitors are known to affect the diagnostics of gastrointestinal disorders. The aim of this study was to investigate to what extent omeprazole, diclofenac or co-administration of these affects faecal calprotectin levels and the normalisation interval after cessation.

Methods
Participants received 20 mg omeprazole daily for 2 weeks in the first sequence, 50 mg oral diclofenac three times daily for 2 weeks in the second and co-administration of these for 2 weeks in the third, with washout periods in between. The first two sequences were randomised to a different order. Faecal calprotectin was measured on days 0, 4, 7, 14, 21, 28 and 35 and thereafter at 7-day intervals until normalisation in each sequence.

Results
Thirty-two healthy volunteers were included. During drug intake, 39% on diclofenac (median 70.8 µg/g; range 50.2–1080 µg/g), 53% on omeprazole (median 85.3 µg/g; range 51.1–249 µg/g) and 69% on omeprazole + diclofenac (median 101.5 µg/g; range 51.5–532 µg/g) had faecal calprotectin levels above normal. In the diclofenac sequence, faecal calprotectin returned to normal in all participants within 2 weeks of cessation and in the omeprazole and co-administration sequences, within 3 weeks of cessation. No statistical significant difference was found with respect to drug order.

Conclusion
Short-term intake of omeprazole, diclofenac or co-administration appears to increase faecal calprotectin levels. In patients with increased faecal calprotectin on omeprazole alone or in combination with diclofenac, a repeated faecal calprotectin test is recommended at least 3 weeks after cessation. On diclofenac alone, it is sufficient to repeat the faecal calprotectin test 2 weeks after cessation.
Retreatment with anti-tumor necrosis factor therapy in combination with an immunomodulator for recurrence of Crohn’s disease after ileocecal resection results in prolonged continuation as compared to anti-tumor necrosis factor monotherapy
Authors: ten Bokkel Huinink Sebastiaan. , Beelen Evelien M.J. , ten Bokkel Huinink Thomas , Hoentjen Frank , G. L. Bodelier Alexander , Dijkstra Gerard , Romberg-Camps Marielle , de Boer Nanne K. , Stassen Laurents P.S. , van der Meulen Andrea E. , West Rachel , van Ruler Oddeke , van der Woude C. Janneke , de Vries Annemarie C. ,   On behalf of the Dutch Initiative on Crohn and Colitis (ICC)
Published: December 2022

Background
A considerable proportion of Crohn’s disease patients that undergo ileocecal resection (ICR) have failed anti-tumor necrosis factor (TNF) therapy preoperatively. This study aimed to assess the effectiveness of retreatment of anti-TNF therapy in patients with postoperative recurrence.

Methods
A real-world cohort study was performed on Crohn’s disease patients who underwent primary ICR after anti-TNF therapy failure, and who were retreated with anti-TNF therapy for postoperative symptomatic Crohn’s disease. The primary outcome was treatment failure (the need for (re)introduction of corticosteroids, immunosuppressants, or biologicals or the need for re-resection). Sub-analyses were performed on the nature of preoperative anti-TNF failure (primary non-response, secondary loss of response, intolerance), indication for ICR (refractory, stricturing, penetrating disease), combination therapy with immunomodulators, retreatment with the same anti-TNF agent and preoperative exposure to 1 vs. >1 anti-TNF agents.

Results
In total, 66 of 364 patients retreated with anti-TNF therapy following ICR. Cumulative rates of treatment failure at 1 and 2 years were 28% and 47%. Treatment failure rate at 2 years was significantly lower in patients receiving combination therapy as compared to anti-TNF monotherapy (30% vs. 49%, P = 0.02). No difference in treatment failure was found with regards to the nature of preoperative anti-TNF failure (P = 0.76), indication for ICR (P = 0.88) switch of anti-TNF agent (P = 0.55) agent, and preoperative exposure to 1 vs. >1 anti-TNF agents (P = 0.88).

Conclusion
Retreatment with anti-TNF therapy for postoperative Crohn’s disease recurrence is a valid strategy after preoperative failure. Combination therapy is associated with a lower rate of treatment failure.
Increased 18F-FAPI PET/CT Uptake in a Case of Brucellosis of Lumbar Vertebral Body
Authors: Mu Xingyu , Zhu Zhuohao , Fu Wei 
Published: December 2022

Abstract
Vertebral brucellosis is a relatively rare disease that usually emerges in animal husbandry areas. We report a case that brucellosis of lumbar vertebral body showed an intense uptake of FAPI on 18F-FAPI PET/CT, which mimics to malignant lesions or vertebral tuberculosis. It is an interesting finding to realize that vertebral brucellosis is also one of the reasons for intense uptake of FAPI.
Increased FDG Uptake in Skin Rashes Caused by EGFR Inhibitors
Authors: Erol Fenercioğlu Özge , Cin Merve , Beyhan Ediz , Şahin Rahime , Çermik Tevfik Fikret 
Published: December 2022

Abstract
Most patients treated with epidermal growth factor receptor inhibitors develop cutaneous advance effects. The extent and severity of treatment-related skin rashes are associated with good treatment response and prognosis. Herein, we presented increased uptake of the 18F-FDG in skin rashes after treatment with epidermal growth factor receptor inhibitors in 2 patients diagnosed with metastatic colorectal cancer.
Post-ERCP Complication Analysis of an Experienced Center
Authors: Ak Çağatay , Aykut Hüseyin , Pala Emin , Sayar Süleyman , Tarikçi Kiliç Ebru , Adali Gupse , Kahraman Resul , Öztürk Oğuzhan , Özdil Kamil 
Published: December 2022

Background/Aim:
Post-ERCP pancreatitis (PEP), post-sphincterotomy bleeding (PSB), and Post-ERCP perforation are the most common complications of endoscopic retrograde cholangiopancreatography (ERCP). Identification of risk factors for post-ERCP complications is critical for postoperative follow-up. This study aimed to evaluate the most common post-ERCP complication risk factors in an experienced center.

Methods/Design:
The sample consisted of 1288 patients with naive papillae. Demographic characteristics, patient-related risk factors, procedure-related risk factors and postoperative complications were recorded.

Results:
Patients had a mean age of 61.5±18.4 years. The prevalence of PEP, PSB, and post-ERCP perforation was 7.9%, 11.9%, and 0.5%, respectively. Among patient-related factors, female sex (OR 1.672 95% Cl 1.046 to 2.672) and narrowing of the choledochal diameter (OR 2.910 95% Cl 1.830 to 4.626) were associated with PEP. From procedure-related factors; precut sphincterotomy (OR 2.172 95% Cl 1.182 to 3.994), difficult cannulation (OR 5.110 95% Cl 2.731 to 9.560), pancreatic cannulation (OR 5.692 95% Cl 0.994 to 32.602) and postprocedure residual stone (OR 2.252 95% Cl 1.403 to 3.614) were found to be associated with PEP. The successful procedure (OR 0.378 95% Cl 0.204 to 0.699) had a protective effect on PEP. Choledocholithiasis indication (OR 3.594 95% Cl 1.444 to 8.942) and small papilla (OR 2.042 95% Cl 1.170 to 3.562) were associated with the development of PSB. Choledochal stenosis, periampullary-diverticulum, oral anticoagulant, and oral antiaggregant use were not associated with the development of PSB. Of the patients with post-ERCP perforation, 85.7% had difficult cannulation, 57.1% had precut sphincterotomy, and 28.6% had periampullary-diverticulum.

Conclusion:
Female sex, biliary stricture, precut sphincterotomy, difficult cannulation, pancreatic cannulation, and postoperative residual stone were associated with PEP. Choledocholithiasis indication and the presence of small papilla were associated with PSB.
Optimization with photonic wave-based annealers
Authors: Prabhakar A. , Shah P. , Gautham U. , Natarajan V. , Ramesh V. , Chandrachoodan N. , Tayur S. 
Published: December 2022

Many NP-hard combinatorial optimization (CO) problems can be cast as a quadratic unconstrained binary optimization model, which maps naturally to an Ising model. The final spin configuration in the Ising model can adiabatically arrive at a solution to a Hamiltonian, given a known set of interactions between spins. We enhance two photonic Ising machines (PIMs) and compare their performance against classical (Gurobi) and quantum (D-Wave) solvers. The temporal multiplexed coherent Ising machine (TMCIM) uses the bistable response of an electro-optic modulator to mimic the spin up and down states. We compare TMCIM performance on Max-cut problems. A spatial photonic Ising machine (SPIM) convolves the wavefront of a coherent laser beam with the pixel distribution of a spatial light modulator to adiabatically achieve a minimum energy configuration, and solve a number partitioning problem (NPP). Our computational results on Max-cut indicate that classical solvers are still a better choice, while our NPP results show that SPIM is better as the problem size increases. In both cases, connectivity in Ising hardware is crucial for performance. Our results also highlight the importance of better understanding which CO problems are most likely to benefit from which type of PIM.
This article is part of the theme issue ‘Quantum annealing and computation: challenges and perspectives’.
Statistics of the number of defects after quantum annealing in a thermal environment
Authors: Suzuki Sei , Oshiyama Hiroki , Shibata Naokazu 
Published: December 2022

We study the statistics of the kink number generated by quantum annealing in a one-dimensional transverse Ising model coupled to a bosonic thermal bath. Using the freezing ansatz for quantum annealing in the thermal environment, we show the relation between the ratio of the second to the first cumulant of the kink number distribution and the average kink density. The theoretical result is confirmed thoroughly by numerical simulation using the non-Markovian infinite time-evolving block decimation which we proposed recently. The simulation using D-Wave’s quantum annealer is also discussed.This article is part of the theme issue ‘Quantum annealing and computation: challenges and perspectives’.