bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine Learning-based Prediction Models for Diagnosis and Prognosis in Inflammatory Bowel Diseases: A Systematic Review
Authors: Nguyen Nghia H , Picetti Dominic , Dulai Parambir S , Jairath Vipul , Sandborn William J , Ohno-Machado Lucila , Chen Peter L , Singh Siddharth 
Published: September 2021

Abstract

Background and Aims
There is increasing interest in machine learning-based prediction models in inflammatory bowel diseases [IBD]. We synthesised and critically appraised studies comparing machine learning vs traditional statistical models, using routinely available clinical data for risk prediction in IBD.

Methods
Through a systematic review till January 1, 2021, we identified cohort studies that derived and/or validated machine learning models, based on routinely collected clinical data in patients with IBD, to predict the risk of harbouring or developing adverse clinical outcomes, and reported its predictive performance against a traditional statistical model for the same outcome. We appraised the risk of bias in these studies using the Prediction model Risk of Bias ASsessment [PROBAST] tool.

Results
We included 13 studies on machine learning-based prediction models in IBD, encompassing themes of predicting treatment response to biologics and thiopurines and predicting longitudinal disease activity and complications and outcomes in patients with acute severe ulcerative colitis. The most common machine learning models used were tree-based algorithms, which are classification approaches achieved through supervised learning. Machine learning models outperformed traditional statistical models in risk prediction. However, most models were at high risk of bias, and only one was externally validated.

Conclusions
Machine learning-based prediction models based on routinely collected data generally perform better than traditional statistical models in risk prediction in IBD, though frequently have high risk of bias. Future studies examining these approaches are warranted, with special focus on external validation and clinical applicability.
The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease
Authors: Bourgonje Arno R , Hu Shixian , Spekhorst Lieke M , Zhernakova Daria V , Vich Vila Arnau , Li Yanni , Voskuil Michiel D , van Berkel Lisette A , Bley Folly Brenda , Charrout Mohammed , Mahfouz Ahmed , Reinders Marcel J T , van Heck Julia I P , Joosten Leo A B , Visschedijk Marijn C , van Dullemen Hendrik M , Faber Klaas Nico , Samsom Janneke N , Festen Eleonora A M , Dijkstra Gerard , Weersma Rinse K 
Published: September 2021

Abstract

Background and Aims
Protein profiling in patients with inflammatory bowel diseases [IBD] for diagnostic and therapeutic purposes is underexplored. This study analysed the association between phenotype, genotype, and the plasma proteome in IBD.

Methods
A total of 92 inflammation-related proteins were quantified in plasma of 1028 patients with IBD (567 Crohn’s disease [CD]; 461 ulcerative colitis [UC]) and 148 healthy individuals to assess protein-phenotype associations. Corresponding whole-exome sequencing and global screening array data of 919 patients with IBD were included to analyse the effect of genetics on protein levels (protein quantitative trait loci [pQTL] analysis). Intestinal mucosal RNA sequencing and faecal metagenomic data were used for complementary analyses.

Results
Thirty-two proteins were differentially abundant between IBD and healthy individuals, of which 22 proteins were independent of active inflammation; 69 proteins were associated with 15 demographic and clinical factors. Fibroblast growth factor-19 levels were decreased in CD patients with ileal disease or a history of ileocecal resection. Thirteen novel cis-pQTLs were identified and 10 replicated from previous studies. One trans-pQTL of the fucosyltransferase 2 [FUT2] gene [rs602662] and two independent cis-pQTLs of C-C motif chemokine 25 [CCL25] affected plasma CCL25 levels. Intestinal gene expression data revealed an overlapping cis-expression [e]QTL-variant [rs3745387] of the CCL25 gene. The FUT2 rs602662 trans-pQTL was associated with reduced abundances of faecal butyrate-producing bacteria.

Conclusions
This study shows that genotype and multiple disease phenotypes strongly associate with the plasma inflammatory proteome in IBD, and identifies disease-associated pathways that may help to improve disease management in the future.
Aortic valve calcification among elderly males from the general population, associated echocardiographic findings, and clinical implications
Authors: Khurrami Lida , Møller Jacob Eifer , Lindholt Jes Sanddal , Dahl Jordi Sancez , Fredgart Maise Hoeigaard , Obel Lasse M , Steffensen Flemming Hald , Urbonaviciene Grazina , Lambrechtsen Jess , Diederichsen Axel Cosmus Pyndt 
Published: September 2021

Abstract

Aims
Aortic valve calcification (AVC) detected by non-contrast computed tomography (NCCT) associates with morbidity and mortality in patients with aortic valve stenosis. However, the importance of AVC in the general population is sparsely evaluated. We intend to describe the associations between AVC score on NCCT and echocardiographic findings as left atrial (LA) dilatation, left ventricular (LV) hypertrophy, aortic valve area (AVA), peak velocity, mean gradient, and aortic valve replacement (AVR) in a population with AVC scores ≥300 AU.

Methods and results
Of 10 471 males aged 65–74 years from the Danish Cardiovascular Screening trial (DANCAVAS), participants with AVC score ≥300 AU were invited for transthoracic echocardiography and 828 (77%) of 1075 accepted the invitation. AVC scores were categorized (300–599, 600–799, 800–1199, and ≥1200 AU). AVR was obtained from registries. AVC was significantly associated with a steady increase in LA dilation (10.5%, 16.3%, 15.8%, 19.6%, P = 0.031), LV hypertrophy (3.9%, 6.6%, 8.9%, 10.1%, P = 0.021), peak velocity (1.7, 1.9, 2.1, 2.8 m/s, P = 0001), mean gradient (6, 8, 11, 19 mmHg, P = 0.0001), and a decrease in AVA (2.0, 1.9, 1.7, 1.3 cm2, P = 0.0001). The area under the curve was 0.79, 0.93, and 0.92 for AVA ≤1.5 cm2, peak velocity ≥3.0 m/s, and mean gradient ≥20 mmHg, respectively, and the associated optimal AVC score thresholds were 734, 1081, and 1019 AU. AVC &gt; 1200 AU was associated with AVR (P &lt; 0.0001).

Conclusion
Among males from the background population, increasing AVC scores were associated with LA dilatation, LV hypertrophy, AVA, peak aortic velocity, mean aortic gradient, and AVR.
Diaphragmatic pacemaker-induced ventricular tachycardia leading to cardiac arrest: a case report
Authors: Dong Tony , Chami Tarek , Janus Scott , Hajjari Jamal , Fernandez Antonio Sotolongo , Josephson Richard 
Published: September 2021

Abstract

Background
Diaphragmatic pacemakers are used to assist respiration in ventilator-dependent patients. Electromagnetic interference with intrinsic cardiac electrical activity is a theoretical risk but has never been reported in the literature. This case highlights a serious complication of cardiac arrest as a result of diaphragmatic pacing.

Case summary
We report a quadriplegic patient with recent diaphragmatic pacemaker implantation who presented with ventricular tachycardia leading to cardiac arrest. Extensive workup was negative for other aetiologies for ventricular arrhythmias. Reduction of the left-sided diaphragmatic pacemaker voltage resulted in cessation of ventricular ectopy.

Discussion
Diaphragmatic pacing at high voltages can cause unwanted transmission of impulses to the cardiac myocytes as a rare complication. This should be noted as a possible complication of intramuscular diaphragmatic pacing, and efforts should be taken to circumvent this risk in the future.
An autoregulation loop infust-1for circular RNA regulation inCaenorhabditis elegans
Authors: Cao Dong 
Published: September 2021

AbstractMany circular RNAs (circRNAs) are differentially expressed in different tissues or cell types, suggestive of specific factors that regulate their biogenesis. Here, taking advantage of available mutation strains of RNA-binding proteins (RBPs) in Caenorhabditis elegans, I performed a screening of circRNA regulation in 13 conserved RBPs. Among them, loss of FUST-1, the homolog of Fused in Sarcoma (FUS), caused downregulation of multiple circRNAs. By rescue experiments, I confirmed FUST-1 as a circRNA regulator. Through RNA sequencing using circRNA-enriched samples, circRNAs targets regulated by FUST-1 were identified globally, with hundreds of them significantly altered. Furthermore, I showed that FUST-1 regulates circRNA formation with only small to little effect on the cognate linear mRNAs. When recognizing circRNA pre-mRNAs, FUST-1 can affect both exon-skipping and circRNA in the same genes. Moreover, I identified an autoregulation loop in fust-1, where FUST-1, isoform a (FUST-1A) promotes the skipping of exon 5 of its own pre-mRNA, which produces FUST-1, isoform b (FUST-1B) with different N-terminal sequences. FUST-1A is the functional isoform in circRNA regulation. Although FUST-1B has the same functional domains as FUST-1A, it cannot regulate either exon-skipping or circRNA formation. This study provided an in vivo investigation of circRNA regulation, which will be helpful to understand the mechanisms that govern circRNA formation.
A grading system for predicting the prognosis of gastric cancer with liver metastasis
Authors: Hori Soshi , Honda Michitaka , Kobayashi Hiroshi , Kawamura Hidetaka , Takiguchi Koichi , Muto Atsushi , Yamazaki Shigeru , Teranishi Yasushi , Shiraso Satoru , Kono Koji , Kamiga Takahiro , Iwao Toshiyasu , Yamashita Naoyuki 
Published: September 2021

Abstract

Objective
The prognosis of patients with liver metastases from gastric cancer is determined using tumor size and number of metastases; this is similar to the factors used for the prediction of liver metastases from colorectal cancer. The relationship between the degree of liver metastasis from gastric cancer and prognosis with reference to the classification of liver metastasis from colorectal cancer was investigated.

Methods
This was a multi-institutional historical cohort study. Among patients with stage IV gastric cancer, who visited the cancer hospitals in Fukushima Prefecture, Japan, between 2008 and 2015, those with simultaneous liver metastasis were included. Abdominal pretreatment computed tomography images were reviewed and classified into H1 (four or less liver metastases with a maximum diameter of ≤5 cm); H2 (other than H1 and H3) or H3 (five or more liver metastases with a maximum diameter of ≥5 cm). The hazard ratio for overall survival according to the H grade (H1, H2 and H3) was calculated using the Cox proportional hazards model.

Results
A total of 412 patients were analyzed. Patients with H1, H2 and H3 grades were 118, 162 and 141, respectively, and their median survival time was 10.2, 5.7 and 3.1 months, respectively (log-rank P &lt; 0.001). The adjusted hazard ratio for overall survival was H1: H2: H3 = reference: 1.39 (95% confidence interval: 1.04–1.85): 1.69 (95% confidence interval: 1.27–2.27).

Conclusions
The grading system proposed in this study was a simple and easy-to-use prognosis prediction index for patients with liver metastasis from gastric cancer.
A disease severity scale for the evaluation of vaccine and other preventive or therapeutic interventions for travellers’ diarrhoea
Authors: Maier Nicole , Riddle Mark S , Gutiérrez Ramiro , Fraser Jamie A , Connor Patrick , Tribble David R , Porter Chad K 
Published: September 2021

Abstract

Background
Travellers’ diarrhoea (TD) is the most common travel-related illness with an estimated 10 million people afflicted annually. Outcome measures to assess the efficacy of primary and secondary TD interventions were historically based on diarrhoea frequency with ≥1 associated gastrointestinal symptom. Furthermore, efficacy determination is often made on the presence or absence of TD, rather than on TD illness severity. Current severity classifications are based on subjective consideration of impact of illness on activity. We sought to develop a standardized scoring system to characterize TD severity to potentially apply as a secondary outcome in future field studies.

Methods
Data on multiple signs and symptoms were obtained from a previously published multisite TD treatment trial conducted by the US Department of Defense (TrEAT TD). Correlation, regression and multiple correspondence analyses were performed to assess impact on activity and a TD severity score was established.

Results
Numerous signs and symptoms were associated with impaired function, with malaise and nausea most strongly associated [odds ratio (OR) 5.9–44.3, P &lt; 0.0001 and OR 2.8–37.1, P &lt; 0.0001, respectively). Based on co-varying symptomatology, a TD severity score accounting for diarrhoea frequency in addition to several signs and symptoms was a better predictor of negative impact on function than any single sign/symptom (X2 = 127.16, P &lt; 0.001). Additionally, there was a significant difference (P &lt; 0.0001) in the mean TD severity score between those with acute watery diarrhoea (3.9 ± 1.9) and those with dysentery or acute febrile illness (6.2 ± 2.0).

Conclusions
The newly developed disease severity score better predicted a negative impact on activity due to TD than did any single sign or symptom. Incorporating multiple parameters into the TD severity score better captures illness severity and moves the field towards current recommendations for TD management by considering symptoms with high functional impact. Further validation of this score is needed in non-military travellers and other settings.
Human gnathostomiasis in Sri Lanka: an underreported disease?
Authors: Musumeci Stefano , Besson Juliette , Allgöwer Andrea , Chappuis François 
Published: September 2021

Abstract
A healthy young man from Sri Lanka, currently living in Switzerland, consulted at the University Hospital of Geneva with a history of painful erythema and swelling of the left forearm. Laboratory tests showed a slight eosinophilia. Western blot serology for Gnathostoma spp, inconclusive at presentation, became positive 2 weeks later.
‘Those first forgotten particles’
Authors: Compston Alastair 
Published: September 2021

Abstract
Chapter 5. ‘Those first forgotten particles: Diatribae duae medico-philosophicae (1659–1687)’ provides a detailed bibliography, using the system described in chapter 4, of sixteen copies of Willis’s first published book in which are included three treatises: 1. De fermentatione; 2. De febribus; and 3. De urinis. The treatises on fermentation and fevers were translated and published in Dutch, together with the short work on scurvy (first published in 1667); and, alone amongst Willis’s writings, the treatise on urines was translated and published in French. These descriptions are preceded by a narrative highlighting the main bibliographic issues that characterize the various editions, states, and issues of these copies. Of these, some are already known but others newly identified. {117 words}
‘Satisfying a mind desirous of truth’
Authors: Compston Alastair 
Published: September 2021

Abstract
Chapter 13, ‘Satisfying a mind desirous of truth: Dr Willis’s practice of physick (1679–1684)’ provides a detailed bibliography, using the system described in chapter 4, of eleven copies of Willis’s treatises in English, books nine to twelve, intended as a single work, variously including treatises 1–13: made up as three copies of treatises 12–13, 7 (Pharmaceutice rationalis, 1679); three copies of treatises 1–6, 9–10 (The remaining medical works, 1681); one copy of treatises 1–7, 9–10, 12–13 (Dr Willis’s practice of physick, 1681); one copy of treatise 11 (Two discourses concerning the soul of brutes, 1683); and three copies of treatises 1–7, 9–13 (Dr Willis’s practice of physick, 1684). These descriptions are preceded by a narrative highlighting the main bibliographic issues that characterize the various editions, states, and issues of these copies. Of these, some are already known but others newly identified. {149 words}
Neurobiology of injury (compression, traction, laceration) and repair, and grading of injuries
Authors: Hart Andrew 
Published: September 2021

Abstract
The functioning nervous system is an integrated system including conscious and subconscious pathways in the brain and spinal cord, the peripheral nerves, and specialized target organs. Efferent and afferent feedback pathways integrate at multiple levels, and there is interplay with mood, life function, growth, and development. The peripheral nervous system provides homeostatic and pain functions, and links the virtual world of our consciousness to the physical body that senses and manipulates the world around us. Injury disconnects the central nervous system from physical reality and induces profound, time-dependent changes at all levels of the system that mostly impede functional restitution after nerve reconstruction. For surgery to optimize outcomes it must be timely, and applied with precision, neurobiological awareness, and aided by adjuvant therapies or technologies that modulate responses within the central nervous system, primary motor and sensory neurons, repair site, distal nerve stump, and target organs.
Brachial plexus injury in the child
Authors: Bains Robert , Kay Simon 
Published: September 2021

Abstract
Obstetric brachial plexus palsy (OBPP) was first described by the Scottish obstetrician William Smellie in 1779 who described, in a newborn, a case of unilateral arm paralysis which rapidly recovered. He attributed this palsy to compression of the axillary nerve against the humerus, probably wrongly in light of subsequent knowledge. The main risk factor for OBPP is high birth weight (&gt;4000 g) and intrapartum shoulder dystocia causing traction on the brachial plexus. It has been demonstrated in cadaveric models that traction on the arm with the neck laterally flexed in the opposite direction causes rupture or avulsion of the brachial plexus. Upper roots are more likely to rupture due to strong ligamentous attachment to the spine whereas the lower roots are more likely to be avulsed. For unknown reasons, however, in the rare circumstance of small babies born breech, upper root avulsion is common. Other risk factors for OBPP include a previous child affected, prolonged labour, instrumented delivery, and multiparity, although each of these may be a surrogate for large birth weight.
Lower limb trauma outcome measures
Authors: Wallace David 
Published: September 2021

Abstract
The management of lower limb-threatening injuries is complex. Advances over the last few decades have provided the ability to salvage complex limb trauma but also have raised concerns that successful complex salvage surgery may not result in overall benefit for the patient. Surgical factors such as bony union, flap success, and a lack of complications are important but are not the sole factors upon which one can guide the patient toward their decision. The patient needs to know how the different treatments may affect their recovery, rehabilitation, return to work, and outcome. This chapter examines the indications and evidence for amputation and salvage by considering the importance of patient and injury-specific factors, biological and physiological variables, quality of life, patient satisfaction, and cost to the individual, hospital, and healthcare provider.
Fractures of the mandible
Authors: Carter Lachlan M. 
Published: September 2021

Abstract
The mandible forms the lower face and supports the teeth, the diaphragm of the floor of mouth, and the mobile tongue. It articulates with the skull base via the temporomandibular joints and is controlled by the muscles of mastication. Fractures of the mandible are common and require accurate reduction and stable fixation, particularly in the dentate patient. The anatomy, pathology, and management of mandible fractures are described in this chapter.
Latissimus dorsi breast reconstruction
Authors: Lee Mark A. 
Published: September 2021

Abstract
The latissimus dorsi flap provides a predictable, reliable, and safe breast reconstruction, and the original description and use of this flap was a defining moment in plastic surgery. It can replace skin loss, soften contours, produce a natural ptotic shape, provide vascularized protection of prosthetic devices, and even be fashioned as a complete reconstruction without implants. Partial breast defects can also be effectively reconstructed with this flap. It can be used in immediate, skin-sparing mastectomy reconstruction or equally in delayed reconstruction. While free tissue transfer, perforator flaps, and modern acellular dermal matrix techniques have been refined over the past decade, the latissimus dorsi flap has provided a safe alternative with the potential for excellent reconstructive results.
The open abdomen
Authors: Khan Omar A. , McGlone Emma Rose , Reddy Marcus 
Published: September 2021

Abstract
This chapter introduces the concept of the open abdomen and describes the various aetiologies of this complex condition, including the rationale for elective laparostomy in damage control surgery and as a treatment for abdominal compartment syndrome. The significance of the open abdomen is described in terms of its local and systemic complications, which form the basis of the established classification. Important considerations in the acute systemic management of patients with this condition are outlined, and methods of temporary abdominal closure are described. Advantages and disadvantages of these alternatives, including the use of negative-pressure wound therapy, are discussed.
Pilonidal disease
Authors: Echlin Kezia , Fleming Andrew 
Published: September 2021

Abstract
Pilonidal disease presents with a range of signs and symptoms: asymptomatic pits in the natal cleft, acute abscesses, chronic disease with persistent, discharging sinuses, or recurrent disease following previous attempts at treatment. It primarily affects the sacrococcygeal region and is a disease of young adults, generally male, and leads to pain, disability, and time lost from work. The treatment for an acute pilonidal abscess is widely accepted to be incision and drainage with the incision placed out of the natal cleft. The treatment of chronic and recurrent disease is contentious with excision and then either healing by secondary intention, primary closure, or flap closure all being suggested alongside other less aggressive approaches aimed at conserving tissue. Currently none of these treatments is ideal, although primary closure in the midline has been shown to be inferior and should not be performed.
Primary aesthetic rhinoplasty
Authors: Ion Lucian 
Published: September 2021

Abstract
Rhinoplasty is the aesthetic surgical intervention that covers the reshaping of the external nasal pyramid. It includes aesthetic and functional aspects, and addresses developmental or acquired pathology. Characteristically, it is associated with significant psychological overlay and due to the complex three-dimensional nasal structure it is the object of intense patient scrutiny involving fine detail from multiple angles. Nasal physiology characteristics dictate that aesthetic alterations can have profound physiological effects that need to be considered carefully in the design and execution of rhinoplasty surgery.
Ligamentous injuries of the hand and wrist
Authors: Heras-Palou Carlos 
Published: September 2021

Abstract
Ligament injuries in the hand and wrist can lead to instability or dislocation of the joint. Instability is manifest by abnormal joint movement with loading and leads to disability through symptoms of pain, weakness or inability to tolerate load acutely and disruption of joint congruity produces arthritis through excessive contact pressure on the joint surface. The anatomy, mechanisms of injury, diagnosis and treatment of ligament injuries are described according to the joints affected.