bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis
Authors: Ewans Lisa J. , Minoche Andre E. , Schofield Deborah , Shrestha Rupendra , Puttick Clare , Zhu Ying , Drew Alexander , Gayevskiy Velimir , Elakis George , Walsh Corrina , Adès Lesley C. , Colley Alison , Ellaway Carolyn , Evans Carey-Anne , Freckmann Mary-Louise , Goodwin Linda , Hackett Anna , Kamien Benjamin , Kirk Edwin P. , Lipke Michelle , Mowat David , Palmer Elizabeth , Rajagopalan Sulekha , Ronan Anne , Sachdev Rani , Stevenson William , Turner Anne , Wilson Meredith , Worgan Lisa , Morel-Kopp Marie-Christine , Field Michael , Buckley Michael F. , Cowley Mark J. , Dinger Marcel E. , Roscioli Tony 
Published: August 2022

AbstractWhole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and costs remain undefined. We investigated differences between diagnostic and cost outcomes of WGS and WES in a cohort with suspected Mendelian disorders. WGS was performed in 38 WES-negative families derived from a 64 family Mendelian cohort that previously underwent WES. For new WGS diagnoses, contemporary WES reanalysis determined whether variants were diagnosable by original WES or unique to WGS. Diagnostic rates were estimated for WES and WGS to simulate outcomes if both had been applied to the 64 families. Diagnostic costs were calculated for various genomic testing scenarios. WGS diagnosed 34% (13/38) of WES-negative families. However, contemporary WES reanalysis on average 2 years later would have diagnosed 18% (7/38 families) resulting in a WGS-specific diagnostic yield of 19% (6/31 remaining families). In WES-negative families, the incremental cost per additional diagnosis using WGS following WES reanalysis was AU$36,710 (£19,407;US$23,727) and WGS alone was AU$41,916 (£22,159;US$27,093) compared to WES-reanalysis. When we simulated the use of WGS alone as an initial genomic test, the incremental cost for each additional diagnosis was AU$29,708 (£15,705;US$19,201) whereas contemporary WES followed by WGS was AU$36,710 (£19,407;US$23,727) compared to contemporary WES. Our findings confirm that WGS is the optimal genomic test choice for maximal diagnosis in Mendelian disorders. However, accepting a small reduction in diagnostic yield, WES with subsequent reanalysis confers the lowest costs. Whether WES or WGS is utilised will depend on clinical scenario and local resourcing and availability.
Analytical representation for the numerical ephemeris of Titan within short time spans
Authors: Xi X. J. , Vienne A. 
Published: August 2022

Context. Numerical integration ephemerides are widely used in research and engineering for their high precision. However, subject to their finite available time spans, their use is limited in theoretical research, such as the studies of rotation and evolution. Previously, we successfully experimented on the analytical representation of the mean longitude of Titan of the Jet Propulsion Laboratory (JPL) ephemeris, as a function of combinations of proper frequencies, and related the results with what is given in the synthetic ephemerides obtained by the Théorie Analytique des Satellites de Saturne (TASS).
Aims. In this study, the analytical representations of the other osculating elements of the JPL Titan ephemeris are accomplished in order to construct the new synthetic representations, which have the advantages of both systems: long-lasting stability, the system details of TASS, and the high precision of JPL.
Methods. A frequency analysis process was used to obtain the proper frequencies, amplitudes, and phases of the two ephemerides in the short term and the semi-long terms. For the proper frequency of the ascending node of Titan, which has a very long period, it is challenging to acquire the exact value, and the formula of TASS was used. The amplitude and phase of long terms were further calculated by a least-squares procedure.
Results. Thanks to the accomplishments of the new synthetic representations of the JPL ephemeris, we report the complete combinations of the osculating elements of Titan. These combinations contain important dynamical information such as the proper frequencies. They will be useful in the theoretical research.
Peeling in generalized harmonic gauge
Authors: Duarte Miguel , Feng Justin , Gasperín Edgar , Hilditch David 
Published: August 2022

Abstract
It is shown that a large class of systems of non-linear wave equations, based on the good–bad–ugly model, admit formal solutions with polyhomogeneous expansions near null infinity. A particular set of variables is introduced which allows us to write the Einstein field equations in generalized harmonic gauge (GHG) as a good–bad–ugly system and the functional form of the first few orders in such an expansion is found by applying the aforementioned result. Exploiting these formal expansions of the metric components, the peeling property of the Weyl tensor is revisited. The question addressed is whether or not the use of GHG, by itself, causes a violation of peeling. Working in harmonic gauge, it is found that log-terms that prevent the Weyl tensor from peeling do appear. The impact of gauge source functions and constraint additions on the peeling property is then considered. Finally, the special interplay between gauge and constraint addition, as well as its influence on the asymptotic system and the decay of each of the metric components, is exploited to find a particular gauge which suppresses this specific type of log-term to arbitrarily high order.
Self-energy corrected DFT-NEGF for conductance in molecular junctions: an accurate and efficient implementation for TRANSIESTA package applied to Au electrodes
Authors: Fallaque Joel G , Rodríguez-González Sandra , Martín Fernando , Díaz Cristina 
Published: August 2022

Abstract
In view of the development and the importance that the studies of conductance through molecular junctions is acquiring, robust, reliable and easy-to-use theoretical tools are the most required. Here, we present an efficient implementation of the self-energy correction to density functional theory non-equilibrium Green functions method for TRANSIESTA package. We have assessed the validity of our implementation using as benchmark systems a family of acene complexes with increasing number of aromatic rings and several anchoring groups. Our theoretical results show an excellent agreement with experimentally available measurements assuring the robustness and accuracy of our implementation.
Accessibility and use of novel methods for predicting physical activity and energy expenditure using accelerometry: a scoping review
Authors: Pfeiffer Karin A , Clevenger Kimberly A , Kaplan Andrew , Van Camp Cailyn A , Strath Scott J , Montoye Alexander H K 
Published: August 2022

Abstract
Use of raw acceleration data and/or ‘novel’ analytic approaches like machine learning for physical activity measurement will not be widely implemented if methods are not accessible to researchers. Objective: This scoping review characterizes the validation approach, accessibility and use of novel analytic techniques for classifying energy expenditure and/or physical activity intensity using raw or count-based accelerometer data. Approach: Three databases were searched for articles published between January 2000 and February 2021. Use of each method was coded from a list of citing articles compiled from Google Scholar. Authors’ provision of access to the model (e.g., by request, sample code) was recorded. Main Results: Studies (N = 168) included adults (n = 143), and/or children (n = 38). Model use ranged from 0 to 27 uses/year (average 0.83) with 101 models that have never been used. Approximately half of uses occurred in a free-living setting (52%) and/or by other authors (56%). Over half of included articles (n = 107) did not provide complete access to their model. Sixty-one articles provided access to their method by including equations, coefficients, cut-points, or decision trees in the paper (n = 48) and/or by providing access to code (n = 13). Significance: The proliferation of approaches for analyzing accelerometer data outpaces the use of these models in practice. As less than half of the developed models are made accessible, it is unsurprising that so many models are not used by other researchers. We encourage researchers to make their models available and accessible for better harmonization of methods and improved capabilities for device-based physical activity measurement.
Label noise and self-learning label correction in cardiac abnormalities classification
Authors: Gallego Vázquez Cristina , Breuss Alexander , Gnarra Oriella , Portmann Julian , Madaffari Antonio , Da Poian Giulia 
Published: August 2022

Abstract

Objective. Learning to classify cardiac abnormalities requires large and high-quality labeled datasets, which is a challenge in medical applications. Small datasets from various sources are often aggregated to meet this requirement, resulting in a final dataset prone to label noise due to inter- and intra-observer variability and different expertise. It is well known that label noise can affect the performance and generalizability of the trained models. In this work, we explore the impact of label noise and self-learning label correction on the classification of cardiac abnormalities on large heterogeneous datasets of electrocardiogram (ECG) signals. Approach. A state-of-the-art self-learning multi-class label correction method for image classification is adapted to learn a multi-label classifier for electrocardiogram signals. We evaluated our performance using 5-fold cross-validation on the publicly available PhysioNet/Computing in Cardiology (CinC) 2021 Challenge data, with full and reduced sets of leads. Due to the unknown label noise in the testing set, we tested our approach on the MNIST dataset. We investigated the performance under different levels of structured label noise for both datasets. Main results. Under high levels of noise, the cross-validation results of self-learning label correction show an improvement of approximately 3% in the challenge score for the PhysioNet/CinC 2021 Challenge dataset and an improvement in accuracy of 5% and reduction of the expected calibration error of 0.03 for the MNIST dataset. We demonstrate that self-learning label correction can be used to effectively deal with the presence of unknown label noise, also when using a reduced number of ECG leads.
Quantum control and quantum speed limits in supersymmetric potentials
Authors: Campbell C , Li J , Busch Th , Fogarty T 
Published: August 2022

Abstract
Supersymmetry allows one to build a hierarchy of Hamiltonians that share the same spectral properties and which are pairwise connected through common super-potentials. The iso-spectral properties of these Hamiltonians imply that the dynamics and therefore control of different eigenstates are connected through supersymmetric intertwining relations. In this work we explore how this enables one to study general dynamics, shortcuts to adiabaticity and quantum speed limits for distinct states of different supersymmetric partner potentials by using the infinite box as an example.
Mitigation of plasma–wall interactions with low-Z powders in DIII-D high confinement plasmas
Authors: Effenberg F. , Bortolon A. , Casali L. , Nazikian R. , Bykov I. , Scotti F. , Wang H.Q. , Fenstermacher M.E. , Lunsford R. , Nagy A. , Grierson B.A. , Laggner F.M. , Maingi R. , the DIII-D Team  
Published: August 2022

Abstract
Experiments with low-Z powder injection in DIII-D high confinement discharges demonstrated increased divertor dissipation and detachment while maintaining good core energy confinement. Lithium (Li), boron (B), and boron nitride (BN) powders were injected in H-mode plasmas (I
p = 1 MA, B
t = 2 T, P
NB = 6 MW, ⟨n
e⟩ = 3.6–5.0 ⋅ 1019 m−3) into the upper small-angle slot divertor for 2 s intervals at constant rates of 3–204 mg s−1. The multi-species BN powders at a rate of 54 mg s−1 showed the most substantial increase in divertor neutral compression by more than an order of magnitude and lasting detachment with minor degradation of the stored magnetic energy W
mhd by 5%. Rates of 204 mg s−1 of boron nitride powder further reduce edge localized mode-fluxes on the divertor but also cause a drop in confinement performance by 24% due to the onset of an n = 2 tearing mode. The application of powders also showed a substantial improvement of wall conditions manifesting in reduced wall fueling source and intrinsic carbon and oxygen content in response to the cumulative injection of non-recycling materials. The results suggest that low-Z powder injection, including mixed element compounds, is a promising new core-edge compatible technique that simultaneously enables divertor detachment and improves wall conditions during high confinement operation.
How has the North Pacific Gyre Oscillation affected peak season tropical cyclone genesis over the western North Pacific from 1965 to 2020?
Authors: Dai Yifei , Wang Bin , Wei Na , Song Jinjie , Duan Yihong 
Published: August 2022

Abstract
The North Pacific Gyre Oscillation (NPGO) is an important mode of decadal variability in North Pacific sea surface temperature (SST) and sea surface height. This study investigated the potential influence of the NPGO on spatial characteristics of peak season (July to October) tropical cyclone genesis (TCG) number over the western North Pacific (WNP) from 1965 to 2020. We show that the NPGO was the first leading empirical orthogonal function mode of North Pacific SST during the peak tropical cyclone season in that time. On a decadal time scale, the NPGO has opposite impacts on TCG in the west and east WNP. The relatively weak positive correlation west of 140° E and the strong negative correlation east of 140° E result in an overall significant negative correlation between the NPGO and WNP total TCG number (r = −0.49), which is much more robust than the relationship between the Pacific Decadal Oscillation and TCG. The critical factors of the NPGO that affect TCG are vertical motion in the west WNP and vertical wind shear (VWS) in the east WNP. The positive NPGO pattern could induce an anomalous off-equatorial vertical circulation, resulting in an upward motion and increased convective precipitation in the west WNP, favoring local TCG. The anomalous convective precipitation enhances the zonal gradient of the atmospheric heat source in the east WNP, increasing VWS. The North Pacific low-level anticyclonic and upper-level cyclonic associated with the NPGO further enhance the VWS in the east WNP and lead to the negative low-level relative vorticity, inhibiting local TCG. This study emphasizes the importance of the climate impact of the NPGO in recent decades. The findings here have significant implications for the decadal prediction of change in WNP TCG.
Dipole dynamics in the point vortex model
Authors: Lydon Karl , Nazarenko Sergey V , Laurie Jason 
Published: August 2022

Abstract
At the very heart of turbulent fluid flows are many interacting vortices that produce a chaotic and seemingly unpredictable velocity field. Gaining new insight into the complex motion of vortices and how they can lead to topological changes of flows is of fundamental importance in our strive to understand turbulence. Our aim is form an understanding of vortex interactions by investigating the dynamics of point vortex dipoles interacting with a hierarchy of vortex structures using the idealized point vortex model. Motivated by its close analogy to the dynamics of quantum vortices in Bose–Einstein condensates, we present new results on dipole size evolution, stability properties of vortex clusters, and the role of dipole–cluster interactions in turbulent mixing in 2D quantum turbulence. In particular, we discover a mechanism of rapid cluster disintegration analogous to a time-reversed self-similar vortex collapse solution.
Regulation of primary seed dormancy by MAJOR LATEX PROTEIN-LIKE PROTEIN329 in Arabidopsis is dependent on DNA-BINDING ONE ZINC FINGER6
Authors: Chong Sher Ney , Ravindran Pratibha , Kumar Prakash P 
Published: August 2022

Abstract
Seeds exhibit primary dormancy to prevent germination under unfavourable conditions. Previous studies have shown that the gibberellin signalling intermediate RGA-LIKE2 (RGL2) forms a transcription factor complex with DNA-BINDING ONE ZINC FINGER6 (DOF6) in regulating seed dormancy in Arabidopsis. Using an RNA-sequencing approach, we identified MAJOR LATEX PROTEIN-LIKE PROTEIN329 (MLP329) as a downstream target of DOF6. MLP329 was found to be a positive regulator of primary seed dormancy, because freshly harvested unstratified mlp329 mutant seeds showed early germination, while unstratified transgenic seeds overexpressing MLP329 showed poor germination. MLP329 expression level was reduced in wild-type seeds upon dry storage and cold stratification. MLP329 expression level was enhanced by DOF6; however, DOF6-dependent MLP329 expression was suppressed in the presence of RGL2. MLP329 expression was enhanced in seeds treated with ABA and auxin IAA. Moreover, the mlp329 mutant seeds exhibited enhanced expression of the GA biosynthetic gene GA1 and suppression of the ABA biosynthetic gene ZEP compared to the overexpression lines. The observed suppression of DOF6-dependent MLP329 expression by RGL2 reveals a possible negative feedback mechanism to modulate seed dormancy. MLP329 also probably enhances the endogenous ABA/GA ratio to positively regulate primary seed dormancy.
The tumor‐repressing effect of CYP27A1 on renal cell carcinoma by 27‐HC arising from cholesterol metabolism
Authors: Zhang Xingming , Yin Xiaoxue , Dai Jindong , Sun Guangxi , Zhang Haoran , Liang Jiayu , Zhao Jinge , Zhu Sha , Chen Junru , Zhu Xudong , Ni Yuchao , Wang Zhipeng , Liu Zhenhua , Chen Ni , Shen Pengfei , Zeng Hao 
Published: August 2022

AbstractAs a key approach to mediate cholesterol metabolism, the role of the CYP27A1/27‐HC axis in renal cell carcinoma (RCC) remains unclear. Analysis of CYP27A1 expression from public databases and metastatic cases in our center suggested that CYP27A1 was obviously downregulated in RCC tissues, and survival analysis further showed its correlation with favorable clinicopathological features and prognosis. In vitro, up and downregulation of CYP27A1 expression in RCC cell lines could definitely illustrate its anticipation involving apoptosis, proliferation, invasion, migration, and clonality. This could be achieved through upregulation of 27‐HC concentration, which mediates the activation of signaling pathways of apoptosis and cell cycle arrest. Further, recovery of CYP27A1 expression could definitely inhibit the proliferation of RCC tumors in vivo. This is the first study to explore the role of the CYP27A1/27‐HC axis in RCC. Attempts to maintain the normal function of the axis may be a potential strategy in the treatment of RCC, and the predictive value of CYP27A1 detection on the efficacy of targeted therapy in metastatic RCC is also worthy of attention.
Disseminated Nocardia otitidiscaviarum presenting as septic arthritis in a nephrotic syndrome patient on immunosuppressants
Authors: Albuni Mhd Kutaiba , Kanjo Wael , El Siddig Awadelkarim Hussein Abdelrahman , Lutf Abdo Qaid Ahmed , Al Samawi Musaed Saad A. , Petkar Hawabibee Mahir 
Published: August 2022

Rationale:
Septic arthritis due to Nocardia is rare, with Nocardia otitidiscaviarum being the rarest Nocardia species isolated from septic arthritis.

Patient concerns:
Here we present a case of a 47-year-old man with a history of nephrotic syndrome on active treatment who developed signs and symptoms of septic arthritis.

Diagnosis:
Initial Laboratory test results showed high inflammatory markers, Right knee joint ultrasound revealed effusion. Therefore, knee arthrocentesis was performed, which revealed a milky orange fluid that grew gram-positive branching forms identified as moderate Nocardia otitidiscaviarum. Despite being asymptomatic, the patient underwent Head computed tomography, which revealed dissemination to the brain.

Intervention:
The patient was started on appropriate antibiotics, immunosuppressant medications were stopped, and arthroscopic drainage was performed.

Outcomes:
Repeated arthrocentesis after 2 weeks was sterile. After 1 month, the patient felt better, pain-free, and was able to ambulate.

Lessons:
Nocardial arthritis is rare, and joint management requires an internist, a rheumatologist, a surgeon, and an infectious disease expert because early identification of the bacteria can improve the outcomes and quality of life.
A rare case of duodenal food bolus impaction mimicking a tumor
Authors: Wang Song-Wei , Hsu Wen-Hung , Wang Jiunn-Wei 
Published: August 2022

Introduction:
Most foreign body and food bolus impactions occur in the upper gastrointestinal tract. Presentation of food bolus impaction in the duodenum without anatomic abnormalities is rare. However, surgical intervention is often required. Diagnosis is difficult. Occasionally, food bolus impaction in the duodenum may be confused with tumor obstruction.

Patient concerns:
A 70-year-old man with no history of abdominal surgery presented with vomiting after meals for 1 day. He also experienced a weight loss of 3 kg on the last fortnight.

Diagnosis:
Abdominal computed tomography revealed duodenal obstruction due to the mass. Upper endoscopy confirmed a diagnosis of food bolus impaction.

Interventions:
Conservative treatment with nasogastric tube decompression and intravenous fluid supply was initially performed, but was unsuccessful. The duodenal food bolus was not retrieved by esophagogastroduodenoscopy. The mass was eventually removed using push enteroscopy.

Outcomes:
The patient’s appetite returned after the food bolus was removed. The patient did not have any gastrointestinal upsets following retrieval. The patient was discharged without complications.

Conclusion:
Contrast-enhanced computed tomography is a practical examination for differentiating intraluminal food bolus from intestinal malignancy in patients with obstruction of the small intestine. Enteroscopy is a suitable modality for duodenal food bolus retrieval owing to its accessibility, efficacy, and safety.