bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Contribution of Partial Meniscectomy to Preoperative Laxity and Laxity After Anatomic Single-Bundle Anterior Cruciate Ligament Reconstruction: In Vivo Kinematics With Navigation
Authors: Grassi Alberto , Di Paolo Stefano , Lucidi Gian Andrea , Macchiarola Luca , Raggi Federico , Zaffagnini Stefano 
Published: October 2019

Background: Limited in vivo kinematic information exists on the effect of clinical-based partial medial and lateral meniscectomy in the context of anterior cruciate ligament (ACL) reconstruction. Hypothesis: In patients with ACL deficiency, partial medial meniscus removal increases the anteroposterior (AP) laxity with compared with those with intact menisci, while partial lateral meniscus removal increases dynamic laxity. In addition, greater postoperative laxity would be identified in patients with partial medial meniscectomy. Study design: Cross-sectional study; Level of evidence, 3. Methods: A total of 164 patients with ACL tears were included in the present study and divided into 4 groups according to the meniscus treatment they underwent: patients with partial lateral meniscectomy (LM group), patients with partial medial meniscectomy (MM group), patients with partial medial and lateral meniscectomy (MLM group), and patients with intact menisci who did not undergo any meniscus treatment (IM group). A further division in 2 new homogeneous groups was made based on the surgical technique: 46 had an isolated single-bundle anatomic ACL reconstruction (ACL group), while 13 underwent a combined single-bundle anatomic ACL reconstruction and partial medial meniscectomy (MM-ACL group). Standard clinical laxities (AP translation at 30° of knee flexion, AP translation at 90° of knee flexion) and pivot-shift (PS) tests were quantified before and after surgery by means of a surgical navigation system dedicated to kinematic assessment. The PS test was quantified through 3 different parameters: the anterior displacement of the lateral tibial compartment (lateral AP); the posterior acceleration of the lateral AP during tibial reduction (posterior acceleration); and finally, the area included by the lateral AP translation with respect to the flexion/extension angle (area). Results: In the ACL-deficient status, the MM group showed a significantly greater tibial translation compared with the IM group ( P < .0001 for AP displacement at 30° [AP30] and 90° [AP90] of flexion) and the LM group ( P = .002 for AP30 and P < .0001 for AP90). In the PS test, the area of LM group was significantly larger (57%; P = .0175) than the one of the IM group. After ACL reconstruction, AP translation at 30° was restored, while the AP90 remained significantly greater at 1.3 mm ( P = .0262) in the MM-ACL group compared with those with intact menisci. Conclusion: Before ACL reconstruction, partial medial meniscectomy increased AP laxity at 30° and 90° and lateral meniscectomy increased dynamic PS laxity with respect to intact menisci. Anatomic single-bundle ACL reconstruction decreased laxities, but a residual anterior translation of 1.3 mm at 90° remained in patients with partial medial meniscectomy, with respect to those with intact menisci.
Scoping Review of Access to Emergency Contraception for Sexual Assault Victims in Emergency Departments in the United States
Authors: Wang Michelle J. , Khodadadi Alexandra B. , Turan Janet M. , White Kari 
Published: October 2019

Objective: We conducted a scoping review of the literature to assess the prevalence of hospital policies regarding emergency contraception (EC) and the frequency that U.S. emergency departments (EDs) provide EC to sexual assault survivors. Study Design: We searched PubMed, Embase, the Cochrane Library, and CINAHL from inception to January 2019 for studies that assessed access to EC for sexual assault survivors in EDs. We included English-language studies that surveyed ED staff at U.S. hospitals and reported the weighted mean of the percentage of hospitals with an EC policy for sexual assault survivors and the percentage that provided EC counseling, offered or dispensed EC onsite. Secondary outcomes were rates of testing and prophylaxis for sexually transmitted infections (STIs) and HIV. Results: From 390 articles retrieved, 14 studies met the inclusion criteria; all studies were published between 2000 and 2013. Eligible studies surveyed staff at 3,314 hospitals. Overall, 60% (weighted mean) of hospitals had a policy on EC, 75% provided EC counseling, 44% offered EC, and 62% had EC available to dispense onsite. Four studies reported secondary outcomes: 81% of hospitals provided STI testing, 84% provided STI prophylaxis, 64% provided HIV testing, and 53% provided HIV prophylaxis. Conclusion: Existing literature demonstrates significant variability in EC policies and practices for sexual assault survivors in U.S. hospital EDs. Future research should assess whether EC access for survivors has improved in ED settings as well as evaluate persistent or new barriers to access.
Characteristics and outcome of patients set up on high-flow oxygen therapy at home
Authors: Dolidon Samuel , Dupuis Johann , Molano Valencia Luis-Carlos , Salaün Mathieu , Thiberville Luc , Muir Jean-François , Cuvelier Antoine , Patout Maxime 
Published: October 2019

Background: High-flow oxygen therapy (HFOT) is increasingly used for acute respiratory failure. Few data support its use at home for the treatment of chronic respiratory failure. Our aim was to report the pattern of the use of long-term HFOT in our center and the outcome of patients setup on long-term HFOT. Methods: A retrospective monocentric study including all patients setup on long-term HFOT between January 2011 and April 2018 in Rouen University Hospital was carried out. Patients were divided into two groups, patients with hypoxemic respiratory failure treated with nasal HFOT (nHFOT) and tracheotomized patients treated with tracheal HFOT (tHFOT). Results: A total of 71 patients were established on long-term HFOT. Out of these 43 (61%) were included in the nHFOT group and 28 (39%) were included in the tHFOT group. In the nHFOT group, underlying respiratory diseases were interstitial lung disease ( n = 15, 35%), pulmonary hypertension ( n = 12, 28%), lung cancer ( n = 9, 21%), and chronic airway disease ( n = 7, 16%). In the tHFOT group, the number of admissions for exacerbation decreased by −0.78 per year (–2 to 0) ( p = 0.045). In total, 51 (72%) patients were discharged to their homes and 20 (28%) went to a post-acute re-enablement facility. Median survival following HFOT was 7.5 months. Survival was significantly lower in the nHFOT group with a median survival of 3.6 months whereas median survival was not reached in the tHFOT group ( p < 0.001). Monthly costs associated with home delivery of HFOT were €476 (296–533) with significant differences in costs between the nHFOT group of €520 (408–628) and costs in the tHFOT group of €296 (261–475) ( p < 0.001). Conclusions: The use of long-term HFOT allows very severe patients to be discharged at a reasonable cost from acute care facilities. The reviews of this paper are available via the supplementary material section.
Acute Kidney Injury in Critically Ill Children and Subsequent Chronic Kidney Disease
Authors: Hessey Erin , Perreault Sylvie , Dorais Marc , Roy Louise , Zappitelli Michael 
Published: October 2019

Background: The progression from acute kidney injury (AKI) to chronic kidney disease (CKD) is not well understood in children. Objectives: We aimed to develop a pediatric CKD definition using administrative data and use it to evaluate the association between AKI in critically ill children and CKD 5 years after hospital discharge. Design: Retrospective cohort study using chart collection and administrative data. Setting: Two-center study in Montreal, Canada. Patients: Children (≤18 years old) admitted to two pediatric intensive care units (ICUs) between 2003 and 2005. We a priori excluded patients with end-stage renal disease or no health care number. Only the first admission during the study period was included. We excluded patients who could not be linked to administrative data, did not survive hospitalization, or had preexisting renal disease. Measurements: Acute kidney injury was defined using Kidney Disease: Improving Global Outcomes (KDIGO) criteria. Patients were defined as having CKD 5 years post-discharge if they had ≥1 CKD diagnostic code or ≥1 CKD-specific medication prescription. Methods: Chart data used to define the exposure (AKI) were merged with provincial administrative data used to define the outcome (CKD). Cox regression was used to evaluate the AKI-CKD association. Results: A total of 2235 (56% male) patients were included, and the median admission age was 3.7 years. A total of 464 (21%) patients developed AKI during pediatric ICU admission. At 5 years post-discharge, 43 (2%) patients had a CKD diagnosis. Patients with both stage 1 and stage 2-3 AKI had increased risk of a CKD diagnosis, with the adjusted hazard ratios (95% confidence intervals) of 2.2 (1.1-4.5) and 2.5 (1.1-5.7), respectively ( P < .001). Limitations: Results may not be generalizable to non-ICU patients. We were not able to control for post-discharge variables; future research should try to explore these additional potential risk factors further. Conclusions: Acute kidney injury is associated with 5-year post-discharge CKD diagnosis defined by administrative health care data.
Provision of Dental Trauma Care in a Remote and Rural Setting
Authors: Gray Crawford , Gupta Varun 
Published: October 2019

Advanced oral surgery such as the treatment of fractures of the mandible is difficult to be performed in rural and remote settings. Within India, the bulk of the population reside in the countryside rather than in urban settings, leading to a lack of provision of secondary care services. Within the Chitrakoot Project, a modern, fully equipped dental surgery has evolved, which with the assistance of Indian specialists from secondary care, and visitors from abroad, has become a rural clinic capable of treating mandibular fractures using maxillomandibular fixation. The concept of training for remote and rural dental surgeons is explored, and three cases are chronicled. The experience in Chitrakoot is something which could be usefully rolled out to suitable rural surgeons to receive training in teaching hospitals, which would improve the provision of acute oral surgery within the rural population of India, and other countries.
Intravenous Iron for the Treatment of Steroid-Refractory Idiopathic Thrombocytopenic Purpura
Authors: Mouabbi Jason , Hadid Tarik , Kafri Zyad 
Published: October 2019

Abstract
Introduction: Idiopathic thrombocytopenic purpura (ITP) is an acquired platelet disorder that is often caused by antibodies against platelet's antigens. Steroids are effective first therapy for ITP. Steroid-refractory ITP is rare and warrant further investigation and treatment. While iron deficiency anemia (IDA) usually presents with thrombocytosis, there are a few reported cases of IDA presenting with unexplained ITP.
Objective: We aim to determine whether the use of intravenous (IV) iron improves platelet count in patients with concomitant steroid-refractory ITP and IDA.
Methods: We identified five patients with IDA who presented to the St. John Hospital and Medical Center between 1/2010 and 12/2017 with unexplained profound thrombocytopenia. They were initially treated with steroids without success. All patients were then treated with a single infusion of iron dextran to replenish their iron stores.
Results: All five patients were African American females of childbearing age and with a history of menorrhagia. All patients had profound iron deficiency defined as iron saturation less than 20% and ferritin less than 15 ng/dL. Four of these patients had profound thrombocytopenia defined as platelets count below 30,000/mm3(table 1). Other causes of thrombocytopenia were ruled out. With IV iron, all patients achieved complete and durable resolution of their thrombocytopenia lasting for at least 6 months (table 2).
Conclusion: The exact mechanism of thrombocytopenia that occurs in patients with IDA is unknown. However, it is suggested that it may be related to the alteration in the activity of iron-dependent enzymes in the cells responsible for megakaryopoiesis and thrombopoiesis. We suggest that patients who present with concomitant steroid-refractory ITP and IDA should receive a trial of IV iron before proceeding with more aggressive therapy such as splenectomy.

Disclosures
No relevant conflicts of interest to declare.
Rivaroxaban or Aspirin As Thromboprophylaxis in Multiple Myeloma
Authors: Campos-Cabrera Gregorio , Mendez-Garcia Esther , Campos-Cabrera Salvador , Campos-Villagomez Jose-Luis , Campos-Cabrera Virgina 
Published: October 2019

Abstract
Hematological cancer has risk of venous thromboembolism of 28 fold compared to sex and age adjusted incidence in general population (JAMA 2005;293:715-722). This risk increases in patients with MM receiving dexamethasone and immunomodulatory drug. Thus, thromboprophylaxis with aspirin in low risk patients and LMWH or warfarin in high risk patients are recommended (Leukemia 2008;22:414-423). Direct oral anticoagulants are promising due to their convenience and costs-effectiveness in preventing VTE in other settings. They have not been extensively studied in myeloma therapy.
From January of 2010 to December of 2017, 105 with MM received thalidomide and dexamethasone based triplet induction therapy, maintenance with thalidomide and creatinine clearance > 30 mL/min. From those, 23 (21.9%) had only an additional risk factor and were randomized 5:1 to receive 100 mg aspirin or 10 mg rivaroxaban until relapse and need another treatment. Doppler ultrasound was performed every six months or as medical indication in all patients and pulmonary CT scan if EP was suspected.
Five patients received rivaroxaban, 3 males and 2 females, median age of 67.5 years; additional factors were obesity in 4 and DM in one. Aspirin was received by 18 patients, 10 males an 8 females, median age 66.8 years; additional factors were obesity in 10, DM in 5, erythropoietin in 3.
No patient in the Rivaroxaban arm developed thrombosis; bleeding episodes were self-limited to the gums and easy bruising; no major bleeding was detected. One patient in the Aspirin arm, with body mass index of 31.22 kg/m2 as an additional risk factor, developed right iliofemoral DVT without PE; he was changed to rivaroxaban at therapeutic doses for six months with resolution of the DVT and then continue with 10 mg dose; bleeding episodes in all patients were similar to the rivaroxaban arm.
In this small group of patients with a low risk factors with an additional one, that could be in an intermediate risk, the use of rivaroxaban showed a good efficiency and security profiles. Either, rivaroxaban or aspirin could be used in this situations and deserve further investigation.

Disclosures
No relevant conflicts of interest to declare.
Alpha-Granules in Resting Human Platelets Are a Spatially Clustered, Single Major Population
Authors: Pokrovskaya Irina D , Storrie Brian , Yadav Shilpi , Rao Amith , McBride Emma , Aronova Maria , Leapman Richard 
Published: October 2019

Abstract
We interrogated in 3D-space the arrangement of alpha-granules and their proteins within 30 human platelets in order to address two central structure/function questions. First, are alpha-granules based on their size, shape and protein content a single population or not, and second, what implications could organelle frequency and organization within the resting platelet have for platelet biogenesis and membrane fusion events in activated platelets? We used serial block face scanning electron microscopy (SBF-SEM) to render in full platelet volume the ultrastructure of alpha-granules, dense granules, mitochondria, canalicular system (CS), and plasma membrane (PM) in 30 platelets, 10 each from 3 donors. Size and shape were measured for 1488 a-granules. Compositional data were assessed for multiple proteins over hundreds of granules by 3D-structured illumination microscopy (SIM) and serial section cryo-immunogold electron microscopy. Data analysis led to 3 conclusions: 1) Based on size, shape and protein composition, there was one major population of alpha-granules in resting human platelets, 2) Alpha-granules clustered tightly together while dense granules were more peripherally located and distal from one another suggesting a spatial arrangement that in the one case supports compound granule fusion and in the other case rapid fusion with the PM, and 3) Based on the weak relationship between platelet size and organelle number and volume, we inferred that platelet biogenesis is likely relatively imprecise with alpha-granule inclusion being more precisely metered than that of other organelles,. These results provide a strong, informative baseline for a-granule structural properties and suggest a spatial clustering of organelles within the resting platelet that may be functionally significant during platelet activation.
Figure. Figure.

Disclosures
No relevant conflicts of interest to declare.
The human phylome
Authors: Huerta-Cepas Jaime , Dopazo Hernán , Dopazo Joaquín , Gabaldón Toni 
Published: October 2019

Abstract
Background:
Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them.

Results:
We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes.

Conclusion:
Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.
ChromaClade: combined visualisation of phylogenetic and sequence data
Authors: Monit Christopher , Goldstein Richard A. , Towers Greg J. 
Published: October 2019

Abstract

Background
Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called ‘sequence gazing’ often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny, since similarities may be due to common descent rather than selection pressure, and because it is important to distinguish between founder effects and convergent evolution. We set out to combine phylogenetic and sequence data to produce evolutionarily insightful visualisations.

Results
We present ChromaClade, a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. We demonstrate applications of ChromaClade to human immunodeficiency virus and influenza A virus datasets, illustrating cases of conservative, adaptive and convergent evolution.

Conclusions
We find this to be a powerful approach for visualising site-wise residue distributions and detecting evolutionary patterns, especially in large datasets. ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade.
Signatures of selection for resistance to Haemonchus contortus in sheep and goats
Authors: Estrada-Reyes Zaira M. , Tsukahara Yoko , Amadeu Rodrigo R. , Goetsch Arthur L. , Gipson Terry A. , Sahlu Tilahun , Puchala Richard , Wang Zaisen , Hart Steve P. , Mateescu Raluca G. 
Published: October 2019

AbstractBackgroundGastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode,Haemonchus contortus. Host genetic variation for resistance toH. contortusallows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies in a candidate gene panel of 100 genes using two different approaches (frequentist and Bayesian) to estimateFst outliers in three different breeds of sheep and goats exposed toH. contortus.ResultsOur results for sheep populations showed SNPs under selection inC3AR1,CSF3,SOCS2,NOS2,STAT5B,TGFB2andIL2RAgenes using frequentist and Bayesian approaches. For goats, SNPs inCD1D,ITGA9,IL12A,IL13RA1, CD86andTGFB2genes were under selection. Common signatures of selection in both species were observed inNOS2,TGFB2andTLR4genes. Directional selection was present in all SNPs evaluated in the present study.ConclusionsA total of 13 SNPs within 7 genes of our candidate gene panel related toH. contortusexposure were identified under selection in sheep populations. For goats, 11 SNPs within 7 genes were identified under selection. Results from this study support the hypothesis that resistance toH. contortusis likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection againstH. contortusinfection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.