bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiation proctitis
Authors: Thompson Hannah , Ali Fadwa , Widmar Maria 
Published: July 2024

Abstract
Radiation-related rectal injury can result in a wide spectrum of symptoms, such as bleeding, alterations in bowel function, fistulas, strictures, and secondary malignancies. Acute radiation proctitis is typically self-limited and responds to interruption of radiation treatment. The most common presentation of chronic radiation proctitis is bleeding, 8–12 months after initiation of radiation therapy. Management consists of a step-up approach beginning with sucralfate enemas, a topical treatment which can be administered at home. Formalin is an effective topical agent for bleeding from chronic radiation proctitis and is administered by a physician, as an outpatient procedure. Interventional strategies such as argon plasma coagulation and hyperbaric oxygen are effective, but labour-intensive. Surgery is associated with high morbidity and mortality and should be reserved for cases that are refractory to medical management, symptomatic fistulae, and surgical emergencies such as perforation.
Statistics
Authors: Karavadra Babu , Haines Richard A. , Sule Medha 
Published: July 2024

Abstract
This chapter focuses on single best answer questions that test knowledge on the medical statistics that is relevant for the MRCOG part 1 examination. A solid understanding of the principles that underpin medical statistics is vital. The practice of evidence based medicine cannot be underestimated. It is important to understand the principles of screening, the levels of evidence and clinical trial design. Patients will often ask about risk, and therefore an understanding of how risk is quantified is important. The ability to interpret statistical tests is an important part of the MRCOG part 1 examination.
Immunology
Authors: Karavadra Babu , Haines Richard A. , Sule Medha 
Published: July 2024

Abstract
This chapter focuses on single best answer questions that test knowledge on the immunology that is relevant for the MRCOG part 1 examination. An understanding of the basic principles that underpin medical immunology is important for clinical practice that underpins obstetrics and gynaecology. For example, fetal haemolysis is an important consideration within the antenatal context; an understanding of the underlying immunology will help to understand this better and provide safe care. Immune system related medical conditions are not uncommon and therefore an understanding of how and why they develop is important. An understanding of basic immunology is important in the context of stillbirth and any respective investigations that are requested to identify a potential cause.
Biophysics
Authors: Karavadra Babu , Haines Richard A. , Sule Medha 
Published: July 2024

Abstract
This chapter focuses on single best answer questions that test knowledge on the biophysics that is relevant for the MRCOG part 1 examination. An understanding of the basic biophysics that underpin the practice of obstetrics and gynaecology is important. An awareness of when the different imaging modalities should be considered, as well as their beneficial and non-beneficial effects is extremely important. As in any area of medicine, patient safety must always be at the forefront of care, an understanding of basic biophysics is vital to achieve this. Knowledge of the different types of suture material used within the specialty is important; particular considerations include the length of time a particular suture takes to dissolve.
Data interpretation
Authors: Karavadra Babu , Haines Richard A. , Sule Medha 
Published: July 2024

Abstract
This chapter focuses on single best answer questions that tests data management that is relevant for the MRCOG part 1 examination. The ability to correctly interpret data is important for patient safety. There are many examples of data interpretation within obstetrics and some of these include a partogram, cardiotocographs (CTGs) and fetal ultrasound scans. Within the context of gynaecology, examples include common endocrinological tests, imaging results and applying them to the clinical context. A good understanding of physiology and pathology is important when interpreting data within the clinical context.
Pharmacology
Authors: Karavadra Babu , Haines Richard A. , Sule Medha 
Published: July 2024

Abstract
This chapter focuses on single best answer questions that test knowledge on the pharmacology that is relevant for the MRCOG part 1 examination. An understanding of the basic principles of pharmacology is important for the practice of obstetrics and gynaecology. Knowledge of the mechanism of action of the various drugs, their indications and contraindications is important as part of patient safety. It is important to know the common side effects of the drugs used within the specialty and how this can impact on the fetus during pregnancy. The principles of pharmacology should not be seen in isolation; often it is combined with knowledge that underpins physiology and biochemistry.
Clinical management
Authors: Karavadra Babu , Haines Richard A. , Sule Medha 
Published: July 2024

Abstract
This chapter focuses on single best answer questions that test knowledge on the clinical management of scenarios that are relevant for the MRCOG part 1 examination. This aspect of the curriculum focuses on applied knowledge within the clinical context. As with any clinical problem, there may be several approaches that can be taken to explore the issues further. However, through direct clinical experience, an understanding of the common presentations that underpin the practice of obstetrics and gynaecology will become clear. The clinical management aspect of the part 1 examination will test your ability to apply your knowledge of the basic sciences to the given clinical context.
Cellular, Tissue, and Body Fluid Fundamentals
Authors: Morchi Ravi 
Published: July 2024

Abstract
This opening chapter is a review of the cellular and physiologic fundamentals of surgery. It starts with cell structure and function, including growth cycles and organelle activity. This is followed by the molecular and cellular components of inflammation, and phases of wound healing. Thereafter the chapter covers essential surgical facts about nutrition in various stressed states, digestion of carbohydrates, protein, and lipids, body fluid composition with electrolyte balance, and acid–base status. Information in this chapter will guide residents through both examination and clinical environments.
Hematology
Authors: Morchi Ravi 
Published: July 2024

Abstract
A review of clinically relevant hematologic principles for the care of surgical patients. It starts with the coagulation cascade, including the different laboratory measures of coagulative function. Then it covers features of blood product transfusion, transfusion reactions, and medical measures to augment hemostasis. Clinically relevant antiplatelets, anticoagulants, and thrombolytics are described, and commonly tested hypercoagulable states and bleeding disorders are reviewed. The chapter closes with high yield facts on dyshemoglobinemias.
Anorectal
Authors: Morchi Ravi 
Published: July 2024

Abstract
The chapter begins with anorectal anatomy and mechanics for storage and controlled defecation. A brief mention of diagnostic tests is followed by sections on constipation, prolapse, proctitis, and the solitary rectal ulcer. The next portion of the chapter focuses on anal neoplasia, including benign lesions, anal canal malignancies, and anal margin malignancies. The clinical approach to hemorrhoids, abscesses, and various types of fistulae is detailed. The chapter ends with management of incontinence, anal fissure, and highlights of other commonly tested perianal pathology.
Liver
Authors: Morchi Ravi 
Published: July 2024

Abstract
Tissue architecture and cellular structure of the liver, including its dual circulation and excretory pathway, are key to its productive and detoxifying role in the human body. Basic imaging modalities are summarized, from where the majority of hepatic pathology is diagnosed. Clinical features and management of the complications of liver failure, including ascites, encephalopathy, portal hypertension, and varices occupy the central portion of the chapter. A comprehensive review of mass lesions follows: cysts, abscesses, benign masses, liver metastases, hepatocellular carcinoma, and intrahepatic cholangiocarcinoma. Focus is on the specifics of diagnosis and treatment for each entity. The chapter closes with principles and operative steps of hepatectomy and liver transplantation.
Pancreas
Authors: Morchi Ravi 
Published: July 2024

Abstract
Embryology, structure, and function of both the exocrine and endocrine components of the pancreas are outlined initially. The diagnosis and treatment principles for acute and chronic pancreatitis, and management of anatomic complications like peripancreatic fluid collections, walled off necrosis, and pseudocysts follows thereafter. Surgical drainage, debridement, and resection options are detailed. The common malignant pancreatic masses, including adenocarcinoma and neuroendocrine variants are each described. A stepwise guide to pancreaticoduodenectomy is next. Serous and mucinous benign and precancerous masses, and their management algorithms, are also reviewed. The chapter closes with a summary of laparoscopic distal pancreatectomy and pancreas transplantation- both solid organ and islet cell.
Breast
Authors: Morchi Ravi 
Published: July 2024

Abstract
The diagnosis and management of breast pathology represents a large portion of the board examination. The tissue and cellular anatomy, neural innervation, and venous and lymphatic network of the breast and axilla are reviewed in the opening portion of the chapter. Indications and mechanisms of breast screening are detailed with particular focus on high-yield facts for the examination. Imaging and biopsy workup of breast lesions is next. Following this is a listing of pertinent benign breast entities, then invasive ductal and lobular cancer, and inflammatory breast cancer. The information is presented for surgical residents to quickly move through the diagnostic algorithm and staging. Relevant facts about carcinoma in situ (ductal, lobular, and Paget’s disease of the nipple) are outlined thereafter. Next is a succinct description of partial mastectomy (lumpectomy) and the various forms of total mastectomy, as well as breast reconstruction options. A large section of the chapter is focused on management of the axillae for occult or overt nodal involvement. Indications for, and components of, chemotherapy and radiation are reviewed. The final portion of the chapter is focused on recurrence and considerations in pregnancy.
Critical Care
Authors: Morchi Ravi 
Published: July 2024

Abstract
This chapter begins with cardiopulmonary principles of critical care and cardiovascular pharmacology geared toward the surgical resident. Subsequently we have a focused review of the different forms of shock and the sequential organ failure assessment (SOFA) score. Following this, common neurologic, pulmonary, and renal critical care entities are each given their own section. Included are high-yield facts on diagnosis and management of elevated intracranial pressure, brain death, acute respiratory distress syndrome (ARDS), and acute kidney injury.
Burn
Authors: Morchi Ravi 
Published: July 2024

Abstract
This brief review of burns is meant to assist the surgeon in clinical and examination environments. It starts by addressing epidermal and dermal anatomy and function. The different types and degrees of burns are outlined. Principles of treatment include fluid resuscitation, nutritional supplementation, escharotomy, and skin graft coverage for control of the systemic inflammatory response. Commonly tested topical antimicrobials are listed. The chapter closes with a targeted summary of chemical and electrical burns, hypothermia, frostbite, inhalation injury, and immune-mediated epidermal disease.
Urology and Gynecology
Authors: Morchi Ravi 
Published: July 2024

Abstract
This chapter reviews basic renal, ureteral, bladder, and urethral anatomy and pathology for the general surgeon preparing for board examination. The fundamental architecture and pathophysiology of disease of the female genital tract is also described, with a focus on high-yield facts. Commonly tested benign and malignant entities, and their treatment, are briefly summarized.
Vitreoretinal lymphoma
Authors: Steffanoni Sara , Mochizuki Manabu , Batchelor Tracy , Carbonell Denise , Zierhut Manfred , Ferry Judith 
Published: July 2024

Abstract
Primary vitreoretinal lymphoma (PVRL) represents &lt;1% of all intraocular tumours. The diagnosis of PVRL is challenging and clinical symptoms often mimic chronic uveitis. Multimodality ocular imaging is useful when there is a suspicion of PVRL, but pathological confirmation is essential. Ninety-five per cent of PVRL cases are diffuse large B-cell lymphomas. Additional morphological analyses performed on the vitreous and aqueous humour have improved the diagnostic yield. Local radiotherapy or intravitreal injection of steroid and/or low doses of methotrexate results in ocular remission in &gt;80% of cases, but there is a high rate of ocular and/or central nervous system (CNS) relapse within 2 years. High-dose intravenous methotrexate, with or without local treatment, is being investigated in PVRL, with the dual aims of obtaining local disease control and preventing CNS relapse. This chapter covers the epidemiology, pathogenesis, diagnosis, and treatment options for PVRL.
Histiocytic tumours of the central nervous system
Authors: Abla Oussama , Picarsic Jennifer 
Published: July 2024

Abstract
Histiocytoses are heterogeneous neoplasms of the haematopoietic system characterized by the accumulation of histiocytes with variable inflammatory infiltrates. The identification of the crucial role of the mitogen-activated protein kinase (MAPK) pathway has opened the door to new targeted therapies. This chapter reviews the central nervous system (CNS) manifestations and treatment of six histiocytic disorders: Langerhans cell histiocytosis (LCH), juvenile xanthogranuloma (JXG), Erdheim–Chester disease (ECD), Rosai–Dorfman–Destombes disease (RDD), and histiocytic sarcoma (HS). CNS involvement occurs in 10–25% of LCH cases and can manifest in tumorous or neurodegenerative forms, which can have different clinical, radiographic, and prognostic implications. Intracranial JXG accounts for 2% of all JXG cases, is more common in males, and is usually leptomeningeal, with frequent concurrent systemic disease. Almost 40% of ECD patients can present with tumourous or neurodegenerative manifestations, and this can affect the brain parenchyma, leptomeninges, and hypothalamic–pituitary axis. RDD CNS lesions are usually tumourous, with meningeal or parenchymal masses without neurodegenerative lesions. Refractory CNS histiocytic neoplasms should lead to the consideration of targeted kinase inhibitor therapies such as BRAF/MEK or ERK inhibitors.
Neurological complications of cell therapies in haematological malignancies
Authors: Hottinger Andreas F. , Ghesquières Hervé , Touat Mehdi 
Published: July 2024

Abstract
Cell therapies comprising haematological stem cell transplantation (HCT) and adoptive T-cell therapies (ACT) have become an essential part in the treatment of an expanding range haematological and non-haematological conditions. HCT involves the intravenous infusion of haematopoietic progenitor cells from the patient (autologous) or from a human leucocyte antigen (HLA)-matched donor (allogeneic). Prior to HTC, the patient typically undergoes high-dose preparative chemotherapy to eradicate residual malignant cells and suppress the immune system. After allogeneic HCT, it is essential to prevent graft rejection and graft-versus-host disease. Management of neurological complications after HCT is challenging. Complications may result from a wide range of factors, including drug-related toxicities, infections from fungi, bacteria, or viruses, metabolic encephalopathies, and immune-mediated disorders, as well as disease recurrence. Neurotoxicity associated with immune effector cell therapy such as chimeric antigen receptor (CAR)-T-cell and bispecific T-cell engager (BiTE) treatments is classified as immune effector cell-associated neurotoxicity syndrome (ICANS). ICANS may develop days to weeks following immune effector cell therapy. It may present as non-localizing symptoms, such as encephalopathy, memory loss and headaches, as well as with focal neurological deficits, including, hemiparesis, ataxia, weakness, and aphasia. Rapid recognition and timely treatment of these neurological complications are essential to reduce the risk of permanent neurological deficits and death.
Neurological complications of white blood cell disorders
Authors: Grisold Wolfgang , Calimeri Teresa , Santomasso Bianca D. 
Published: July 2024

Abstract
Disorders of white blood cells can cause a variety of neurological complications. Hyperviscosity syndrome is caused by hyperviscous blood, plasma, or serum and occurs in several haematological disorders. Waldenström’s macroglobulinaemia is the most common cause of hyperviscosity syndrome, followed by immunoglobulin A (IgA) and immunoglobulin G3 (IgG3) multiple myeloma, with a serum paraprotein concentration of over 8 g/dl. Symptoms of hyperviscosity syndrome include mucocutaneous bleeding and ophthalmological and neurological symptoms, including headache, vertigo, nystagmus, dizziness, tinnitus, hearing loss, diplopia, and ataxia. Hyperviscosity syndrome rarely causes confusion, dementia, disturbances of consciousness, stroke, and coma. There is no correlation between measured blood or serum viscosity and clinical symptomatology. Management of hyperviscosity syndrome consists of plasmapheresis for symptomatic improvement followed by concurrent initiation of chemotherapy. Bing–Neel syndrome, a rare disease manifestation of Waldenström’s macroglobulinaemia, characterized by infiltration of lymphoplasmacytic cells into the central nervous system, should be considered in the differential diagnosis of hyperviscosity syndrome. Amyloid and amyloidosis comprise a wide range of conditions, affecting the peripheral nervous system and, to a lesser extent, the central nervous system. AL amyloidosis occurs in monoclonal gammopathies, multiple myeloma, plasmacytoma, Waldenström’s macroglobulinaemia, chronic lymphocytic lymphoma, and other low-grade lymphomas. The most frequent peripheral nervous system lesions are generalized neuropathy and carpal tunnel syndrome, often combined with autonomic dysfunction. Other focal lesions can affect cranial nerves, nerve roots, the plexus, and individual nerves. Amyloidoma and muscle involvement are rare. Local amyloidosis can mimic peripheral nerve lesions. Involvement of the musculoskeletal system, including joints and fascia, has been reported. The central nervous system is less frequently affected, although brain and spinal amyloidomas have been described.
Multifunctional 3D matrixes based on flexible bioglass nanofibers for potential application in postoperative therapy of osteosarcoma
Authors: Wang Lihuan , Yuan Liting , Dong Yanbing , Huang Wenli , Zhu Jichang , Du Xuexian , Zhang Chenglin , Liu Pengbi , Mo Jinpeng , Li Bingyan , Liu Zijin , Yu Xi , Yu Hui 
Published: July 2024

Abstract
Postoperative treatment of osteosarcoma is one of the major challenging clinical issues since both elimination of residual tumors and acceleration of bone regeneration should be considered. Photothermal therapy has been widely studied due to its advantages of small side-effect, low-toxicity, high local selectivity and noninversion, and bone tissue engineering is an inevitable trend in postoperative treatment of osteosarcoma. In this study, we combined the tissue engineering and photothermal therapy together, and developed a kind of multifunctional nanofibrous 3D matrixes for postoperative treatment of osteosarcoma. The flexible bioactive glass nanofibers (BGNFs) prepared by sol–gel electrospinning and calcination acted as the basic blocks, and the genipin-crosslinked gelatin (GNP-Gel) acted as the cement to bond the BGNFs forming a stable 3D structure. The stable porous 3D scaffolds were obtained through ice crystal templating method and freeze-drying technology. The obtained GNP-Gel/BGNF 3D matrixes showed a nanofibrous structure that highly biomimetics the extracellular matrix. The excellent compression recovery performance in water of these matrixes made them suitable for minimally invasive surgery. In addition, these 3D matrixes were not only biocompatible in vitro, but also benefit for the formation of mineralized bone in vivo. Furthermore, the dark blue GNP-Gel also acted as the photothermal agent, which endowed the GNP-Gel/BGNF 3D matrixes with efficient photothermal antitumor and photothermal antibacterial performance without addition of other toxic photothermal agents. Therefore, this study provides an ingenious avenue to prepare multifunctional nanofibrous 3D matrixes with photothermal therapy for postoperative treatment of osteosarcoma.
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny
Authors: Ye Yongtao , Shum Marcus H , Wu Isaac , Chau Carlos , Zhao Ningqi , Smith David K , Wu Joseph T , Lam Tommy T 
Published: July 2024

Abstract
The unprecedentedly large size of the global SARS-CoV-2 phylogeny makes any computation on the tree difficult. Lineage identification (e.g. the PANGO nomenclature for SARS-CoV-2) and assignment are key to track the virus evolution. It requires annotating clade roots of lineages to unlabeled ancestral nodes in a phylogenetic tree. Then the lineage labels of descendant samples under these clade roots can be inferred to be the corresponding lineages. This is the ancestral lineage annotation problem, and matUtils (a package in pUShER) and PastML are commonly used methods. However, their computational tractability is a challenge and their accuracy needs further exploration in huge SARS-CoV-2 phylogenies. We have developed an efficient and accurate method, called “F1ALA”, that utilizes the F1-score to evaluate the confidence with which a specific ancestral node can be annotated as the clade root of a lineage, given the lineage labels of a set of taxa in a rooted tree. Compared to these methods, F1ALA achieved roughly an order of magnitude faster yet with ∼12% of their memory usage when annotating 2277 PANGO lineages in a phylogeny of 5.26 million taxa. F1ALA allows real-time lineage tracking to be performed on a laptop computer. F1ALA outperformed matUtils (pUShER) with statistical significance, and had comparable accuracy to PastML in tests on empirical and simulated data. F1ALA enables a tree refinement by pruning taxa with inconsistent labels to their closest annotation nodes and re-inserting them back to the pruned tree to improve a SARS-CoV-2 phylogeny with both higher log-likelihood and lower parsimony score. Given the ultrafast speed and high accuracy, we anticipated that F1ALA will also be useful for large phylogenies of other viruses. Codes and benchmark datasets are publicly available at https://github.com/id-bioinfo/F1ALA.