bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypoxia during incubation does not affect aerobic performance or haematology of Atlantic salmon (Salmo salar) when re-exposed in later life
Authors: Wood Andrew T , Andrewartha Sarah J , Elliott Nicholas G , Frappell Peter B , Clark Timothy D 
Published: October 2019

AbstractHypoxia in aquatic ecosystems is becoming increasingly prevalent, potentially reducing fish performance and survival by limiting the oxygen available for aerobic activities. Hypoxia is a challenge for conserving and managing fish populations and demands a better understanding of the short- and long-term impacts of hypoxic environments on fish performance. Fish acclimate to hypoxia via a variety of short- and long-term physiological modifications in an attempt to maintain aerobic performance. In particular, hypoxia exposure during early development may result in enduring cardio-respiratory modifications that affect future hypoxia acclimation capacity, yet this possibility remains poorly investigated. We incubated Atlantic salmon (Salmo salar) in normoxia (~100% dissolved oxygen [DO, as percent air saturation]), moderate hypoxia (~63% DO) or cyclical hypoxia (100–25% DO daily) from fertilization until 113 days post-fertilization prior to rearing all groups in normoxia for a further 8 months. At ~11 months of age, subsets of each group were acclimated to hypoxia (50% DO) for up to 44 days prior to haematology, aerobic metabolic rate and hypoxia tolerance measurements. Hypoxia exposure during incubation (fertilization to 113 days post-fertilization) did not affect the haematology, aerobic performance or hypoxia tolerance of juvenile salmon in later life. Juveniles acclimated to hypoxia increased maximum aerobic metabolic rate and aerobic scope by ~23 and ~52%, respectively, when measured at 50% DO but not at 100% DO. Hypoxia-incubated juveniles also increased haematocrit and haemoglobin concentration but did not affect acute hypoxia tolerance (critical oxygen level and DO at LOE). Thus, while Atlantic salmon possess a considerable capacity to physiologically acclimate to hypoxia by improving aerobic performance in low oxygen conditions, we found no evidence that this capacity is influenced by early-life hypoxia exposure.
An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)
Authors: Farré Marta , Li Qiye , Darolti Iulia , Zhou Yang , Damas Joana , Proskuryakova Anastasia A , Kulemzina Anastasia I , Chemnick Leona G , Kim Jaebum , Ryder Oliver A , Ma Jian , Graphodatsky Alexander S , Zhang Guoije , Larkin Denis M , Lewin Harris A 
Published: October 2019

Abstract

Background
The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.

Findings
Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions.

Conclusions
We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.
Nutation terms adjustment to VLBI and implication for the Earth rotation resonance parameters
Authors: Nurul Huda I , Lambert S , Bizouard C , Ziegler Y 
Published: October 2019

SUMMARY
The nutation harmonic terms are commonly determined from celestial pole offset series produced from very long baseline interferometry (VLBI) time delay analysis. This approach is called an indirect approach. As VLBI observations are treated independently for every session, this approach has some deficiencies such as a lack of consistency in the geometry of the session. To tackle this problem, we propose to directly estimate nutation terms from the whole set of VLBI time delays, hereafter referred as a direct approach, in which the nutation amplitudes are taken as global parameters. This approach allows us to reduce the correlations and the formal errors and gives significant discrepancies for the amplitude of some nutation terms. This paper is also dedicated to the determination of the Earth resonance parameters, named polar motion, free core nutation, and free inner core nutation. No statistically significant difference has been found between the estimates of resonance parameters based upon ‘direct’ and ‘indirect’ nutation terms. The inclusion of a complete atmospheric-oceanic non-tidal correction to the nutation amplitudes significantly affected the estimates of the free core nutation and the free inner core nutation resonant frequencies. Finally, we analyzed the frequency sensitivity of polar motion resonance and found that this resonance is mostly determined by the prograde nutation terms of period smaller than 386 d.
Impact of Bariatric Surgery on the Long-term Disease Course of Inflammatory Bowel Disease
Authors: Braga Neto Manuel B , Gregory Martin H , Ramos Guilherme P , Bazerbachi Fateh , Bruining David H , Abu Dayyeh Barham K , Kushnir Vladimir M , Raffals Laura E , Ciorba Matthew A , Loftus Edward V , Deepak Parakkal 
Published: October 2019

AbstractBackgroundAn association between inflammatory bowel disease (IBD) and obesity has been observed. Little is known about the effect of weight loss on IBD course. Our aim was to determine the impact of bariatric surgery on long-term clinical course of obese patients with IBD, either Crohn's disease (CD) or ulcerative colitis (UC).MethodsPatients with IBD who underwent bariatric surgery subsequent to IBD diagnosis were identified from 2 tertiary IBD centers. Complications after bariatric surgery were recorded. Patients were matched 1:1 for age, sex, IBD subtype, phenotype, and location to patients with IBD who did not undergo bariatric surgery. Controls started follow-up at a time point in their disease similar to the disease duration in the matched case at the time of bariatric surgery. Inflammatory bowel disease medication usage and disease-related complications (need for corticosteroids, hospitalizations, and surgeries) among cases and controls were compared.ResultsForty-seven patients met inclusion criteria. Appropriate matches were found for 25 cases. Median follow-up among cases (after bariatric surgery) and controls was 7.69 and 7.89 years, respectively. Median decrease in body mass index after bariatric surgery was 12.2. Rescue corticosteroid usage and IBD-related surgeries were numerically less common in cases than controls (24% vs 52%; odds ratio [OR], 0.36; 95% confidence interval [CI], 0.08–1.23; 12% vs 28%; OR, 0.2; 95% CI, 0.004–1.79). Two cases and 1 control were able to discontinue biologics during follow-up.ConclusionsInflammatory bowel disease patients with weight loss after bariatric surgery had fewer IBD-related complications compared with matched controls. This observation requires validation in a prospective study design.
Relationships between temperament, meat quality, and carcass traits in Nellore cattle1
Authors: Sant’anna Aline Cristina , Valente Tiago Da Silva , Magalhães Ana Fabrícia Braga , Espigolan Rafael , Ceballos Maria Camila , de Albuquerque Lucia Galvão , Paranhos da Costa Mateus José Rodrigues 
Published: October 2019

Abstract
The aim of this study was to evaluate the relationship between temperament in Nellore bulls with carcass and meat quality traits. In total, 1,400 bulls were studied, and temperament was assessed using two measurements: movement score (MOV) and flight speed test (FS). Both MOV and FS were measured at two time points, with background (MOVb and FSb) temperament measured at yearling age, ~550 d after birth, and the preslaughter (MOVps and FSps) temperament measured at the end of the feedlot period. The change of temperament resulting in an increase or decrease in reactivity was also used to measure meat quality. The traits used to define carcass and meat quality included carcass bruises (BRU), hot carcass weight (HCW, kg), ribeye area (REA, cm2), backfat thickness (BFT, cm), marbling score (MS), meat pH after thawing (pH), presence or absence of dark cutters, color parameters of luminosity (L*), redness (a*) and yellowness (b*), cooking loss (CL, %), and Warner–Bratzler shear force (WBSF, kg). A principal component (PC) analysis was initially applied to the carcass and meat quality traits, followed by logistic regression models and linear mixed models to evaluate the effects of temperament on carcass and meat quality. The risks of carcass bruises and dark cutters did not differ as a function of any temperament trait (P &gt; 0.05). In turn, animals classified as high MOVb (reactive) had lower PC3 values (P = 0.05), CL (P = 0.02), and tended to have lower MS (P = 0.08). In addition, animals classified as high FSb (faster and reactive cattle) produced carcasses with smaller REA (P &lt; 0.01), higher meat pH (P &lt; 0.01), lower color gradients (L*, P = 0.04; b*, P &lt; 0.01), and lower PC1 and PC4 scores (P &lt; 0.01) when compared with the low FSb class. For preslaughter temperament, high MOVps was related to lower color a* (P = 0.04), whereas high FSps was related to lower HCW, MS, and PC2 (P &lt; 0.01) than the calmer ones (low FSps). The reduction in MOV was related to more tender meat, and the reduction in FS to heavier carcass and brighter meat. We conclude that excitable temperament in Nellore cattle may have negative effects in some of the carcass and meat quality attributes assessed, mainly those related to muscle deposition on carcass and color gradients. Measurement of temperament before the cattle entered the feedlot was a better predictor of carcass and meat quality traits, compared with temperament assessment at the end of the feeding period.
Objective Value Is Always Newcombizable
Authors: Ahmed Arif , Spencer Jack 
Published: October 2019

Abstract
This paper argues that evidential decision theory is incompatible with options having objective values. If options have objective values, then it should always be rationally permissible for an agent to choose an option if they are certain that the option uniquely maximizes objective value. But, as we show, if options have objective values and evidential decision theory is true, then it is not always rationally permissible for an agent to choose an option if they are certain that the option uniquely maximizes objective value.
Retinoblastoma in children: a case series from Senegal
Authors: Dial Chérif , Doh Kwame , Thiam Ibou , Roth Paul Aïda Ndoye , Moreira Claude , Woto-Gaye Gisèle 
Published: October 2019

AbstractRetinoblastoma is the most common tumor of the eye in Senegalese children. Diagnosis occurs often at a late stage, when enucleation is unavoidable. In this report, we describe all recorded cases occurring in Senegal over a 10-year period (2005–14).For the 106 cases clinically and radiological identified, the mean age at diagnosis was 30 months (2 months / 10 years). Leucocoria (74.6%) and exophthalmos (42.3%) were common signs of the disease. For the 67 cases identified through patient-file examination, extra-ocular forms were present in 30% of cases at the time of diagnosis and retinal detachment in 19% of cases. Chemotherapy and surgery were the only available therapeutic methods. Overall survival at 5 years was 70%.Retinoblastoma is a serious illness that threatens the lives and sight of affected children. There are about 10 cases per year in Senegal. Management can be enhanced by improving existing technical platforms and training medical staff.
One Hundred Eleven Percutaneous Balloon Compressions for Trigeminal Neuralgia in a Cohort of 66 Patients with Multiple Sclerosis
Authors: Asplund Pär , Linderoth Bengt , Lind Göran , Winter Jaleh , Bergenheim A Tommy 
Published: October 2019

Abstract

BACKGROUND
Trigeminal neuralgia associated with multiple sclerosis (MS–TN) is comparatively rare and larger series of percutaneous balloon compression (PBC) in such cases are few in the literature.

OBJECTIVE
To evaluate the results after PBC for MS–TN with regards to therapeutic effect, side effects, and complications.

METHODS
One hundred eleven procedures with PBC performed in 66 cases of MS–TN were analyzed. Therapeutic effect was measured as postoperative time to pain recurrence without medication. All complications were compiled and the sensory function was evaluated in a subgroup of cases.

RESULTS
The initial pain free rate was 67% and the median time to pain recurrence was 8 mo. Thirty-six patients were treated with PBC only, and among them, the results were worse if treated 3 to 4 times before, compared to first treatment (P = .009-.034). Patients who had several PBCs had worse results already after the first surgery (P < .001). A significant number of patients had impaired sensation to light touch directly after surgery, which was normalized at the late follow-up. Sensimetric testing showed raised thresholds for perception and pain directly after surgery (P = .004-.03), but these were also normalized at the late follow-up.

CONCLUSION
PBC is a treatment that can be effective for many patients with MS–TN. Repeated previous surgeries is a risk factor for an unsatisfactory outcome. However, the patients with multiple surgeries had less satisfactory results already at the first procedure, indicating that a therapy resistant disease can be predicted after the first two PBCs. Postoperative sensory deficits were common but not lasting.
Cervical 3 to Cervical 6 Laminectomy for Arteriovenous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: October 2019

Abstract
According to the Spetzler spinal cord classification system,
1
this patient had an extradural-intradural arteriovenous malformation (AVM), also known as a type III or juvenile AVM. The patient underwent a surgical resection of the lesion via a cervical 3 to cervical 6 laminoplasty. Direct observation confirmed intra- and extramedullary components. During the surgical resection, an attempt was made to avoid transgressing the pia mater. Therefore, the traversing vessels were interrupted during the circumdissection. The nidus was removed, and postprocedural digital subtraction angiography confirmed complete obliteration. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Bonnet Bypass for Left Superficial Temporal Artery Bifurcation to Right Middle Cerebral Artery: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: October 2019

Abstract
A bonnet bypass is a long interposition graft bypass used for extracranial to intracranial revascularization, which is useful in patients who do not have a suitable ipsilateral donor or in whom the ipsilateral donor must be sacrificed. This interposition graft is commonly the radial artery or saphenous vein. The only practical difference in this technique for revascularization is that an interposition graft must pass through the subgaleal space to the contralateral scalp to allow for reimplantation at the desired contralateral point of anastomosis. This patient underwent a bonnet bypass for revascularization of the middle cerebral artery (MCA) perfusion territory utilizing the contralateral superficial temporal artery (STA). A saphenous vein was used as the interposition graft, which was anastomosed to an M2 segment bifurcation. The graft was then temporarily occluded and passed within a calvarial trough to the contralateral frontoparietal region. The graft was then anastomosed to the contralateral STA at a bifurcation to accommodate the graft size mismatch. The patient tolerated the bypass procedure well and demonstrated bypass patency on postoperative angiographic imaging. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Beyond squeezing à la Virasoro algebra
Authors: Katagiri So , Sugamoto Akio , Yamaguchi Koichiro , Yumibayashi Tsukasa 
Published: October 2019

Abstract
The generalization of squeezing is realized in terms of the Virasoro algebra. The higher-order squeezing can be introduced through the higher-order time-dependent potential, in which the standard squeezing operator is generalized to higher-order Virasoro operators. We give a formula that describes the number of particles generated by the higher-order squeezing when a parameter specifying the degree of squeezing is small. Formula (18) shows that the higher the order of squeezing, the larger the number of generated particles.
A Streamlined and High-Throughput Error-Corrected Next-Generation Sequencing Method for Low Variant Allele Frequency Quantitation
Authors: McKinzie Page B , Bishop Michelle E 
Published: October 2019

Abstract
Quantifying mutant or variable allele frequencies (VAFs) of ≤10−3 using next-generation sequencing (NGS) has utility in both clinical and nonclinical settings. Two common approaches for quantifying VAFs using NGS are tagged single-strand sequencing and duplex sequencing. While duplex sequencing is reported to have sensitivity up to 10−8 VAF, it is not a quick, easy, or inexpensive method. We report a method for quantifying VAFs that are ≥10−4 that is as easy and quick for processing samples as standard sequencing kits, yet less expensive than the kits. The method was developed using PCR fragment-based VAFs of Kras codon 12 in log10 increments from 10−5 to 10−1, then applied and tested on native genomic DNA. For both sources of DNA, there is a proportional increase in the observed VAF to input VAF from 10−4 to 100% mutant samples. Variability of quantitation was evaluated within experimental replicates and shown to be consistent across sample preparations. The error at each successive base read was evaluated to determine if there is a limit of read length for quantitation of ≥10−4, and it was determined that read lengths up to 70 bases are reliable for quantitation. The method described here is adaptable to various oncogene or tumor suppressor gene targets, with the potential to implement multiplexing at the initial tagging step. While easy to perform manually, it is also suited for robotic handling and batch processing of samples, facilitating detection and quantitation of genetic carcinogenic biomarkers before tumor formation or in normal-appearing tissue.
Inhibition of Endothelial Dysfunction by Dietary Flavonoids and Preventive Effects Against Cardiovascular Disease
Authors: Yamagata Kazuo , Yamori Yukio 
Published: October 2019

Abstract:
Cardiovascular disease (CVD), such as stroke, ischemic heart disease, and heart failure, accounts for many deaths, and its increasing incidence is a worldwide concern. Accumulating evidence suggests that the elevated risk of CVD caused by dysfunction of vascular endothelial cells and resultant arteriosclerosis can be mitigated by increased consumption of fruits and vegetables. These foods contain phytochemicals such as polyphenols and carotenoids, as well as dietary fiber. Flavonoids of the polyphenol class are found in vegetables, fruits, grains, bark, roots, stems, flowers, tea, and wine. Several studies have indicated that flavonoids reduce CVD mortality by inhibiting endothelial dysfunction. Flavonoids have a common carbon skeleton and are classified as flavonols, flavones, flavanols, flavanones, anthocyanidins, and isoflavones. In this review, we discuss recent progress in identifying the mechanisms by which dietary flavonoids improve vascular endothelial cell function. Furthermore, we describe the beneficial role that these flavonoids may play in preventing CVD caused by endothelial dysfunction-related atherosclerosis.
Impact of Continuous P2Y12 Inhibition Tailoring in Acute Coronary Syndrome and Genetically Impaired Clopidogrel Absorption
Authors: Samardzic Jure , Bozina Nada , Skoric Bosko , Ganoci Lana , Krpan Miroslav , Petricevic Mate , Pasalic Marijan , Bozina Tamara , Pavasovic Sasa , Cikes Maja , Milicic Davor 
Published: October 2019

Abstract:
Clopidogrel is still widely used in acute coronary syndrome despite the development of more potent P2Y12 inhibitors. Previously, we conducted a trial that evaluated serial clopidogrel dose adjustment based on platelet function testing in acute coronary syndrome patients with initial high on-treatment platelet reactivity (HTPR). In this substudy, we performed post hoc analysis of the effect of ABCB1 genetic variants C3435T and G2677T/A on platelet inhibition and outcomes. There were no differences in the proportion of HTPR patients among C3435T carriers and noncarriers in both interventional and control group. G2677T carriers expressed significantly higher proportion of HTPR pattern throughout 12-month follow-up in the control group with no difference in the interventional group. There was no difference in ischemic outcomes between C3435T and G2677T carriers and noncarriers in both groups of patients. The results indicate that ABCB1 genotyping is not useful to guide clopidogrel therapy tailoring to improve high-risk patient management.
Effects of Rivaroxaban on Platelet Aggregation
Authors: Hernandez-Juarez Jesus , Espejo-Godinez Hugo Guillermo , Mancilla-Padilla Rodrigo , Hernandez-Lopez Jose Rubicel , Moreno Jose Antonio Alvarado , Majluf-Cruz Karim , Moreno-Hernández Manuel , Isordia-Salas Irma , Majluf-Cruz Abraham 
Published: October 2019

Abstract:
Rivaroxaban is a direct oral anti-factor Xa anticoagulant. It has recently been suggested that rivaroxaban may affect platelet function in vitro; however, little is known about the clinical impact of this likely antiplatelet effect and whether this probable phenomenon is dose-dependent. Our aim was to determine whether rivaroxaban at 4 different doses inhibits direct platelet aggregation. We included adult patients of both sexes and who were allocated to one of the following groups depending on the prescribed daily dose of rivaroxaban: 5, 10, 15, and 20 mg. In 80 patients (20 patients/group), the percentage of platelet aggregation was determined by means of platelet aggregometry tests before and after rivaroxaban use. Basal samples were obtained before starting rivaroxaban and 1 month after treatment, both 2 and 24 hours after the last dose of the drug (12 hours after in the case of rivaroxaban 5 mg). We used 5 platelet agonists: adenosine diphosphate, epinephrine, arachidonic acid, collagen, and thrombin. There were no significant changes in the percentage of platelet aggregation before and after rivaroxaban use independently of the dose administered and the agonist used. Our results have clearly shown that rivaroxaban, even at a high dose, does not directly affect platelet aggregation.