bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluid simulations of cosmic ray-modified shocks
Authors: Tsung Tsun Hin Navin , Oh S Peng , Jiang(姜燕飞) Yan-Fei 
Published: July 2021

ABSTRACT
Cosmic ray (CR)-modified shocks are a demanding test of numerical codes. We use them to test and validate the two-moment method for CR hydrodynamics, as well as characterize the realism of CR shock acceleration in two-fluid simulations which inevitably arises. Previously, numerical codes were unable to incorporate streaming in this demanding regime, and have never been compared against analytic solutions. First, we find a new analytic solution highly discrepant in acceleration efficiency from the standard solution. It arises from bi-directional streaming of CRs away from the subshock, similar to a Zeldovich spike in radiative shocks. Since fewer CRs diffuse back upstream, this favours a much lower acceleration efficiency, typically ${\lesssim}10{{\ \rm per\ cent}}$ (even for Mach number &gt; 10) as opposed to ${\gtrsim}50{{\ \rm per\ cent}}$ found in previous analytic work. At Mach number ≳10, the new solution bifurcates into three branches, with efficient, intermediate, and inefficient CR acceleration. Our two-moment code accurately recovers these solutions across the entire parameter space probed, with no ad hoc closure relations. For generic initial conditions, the inefficient branch is robustly chosen by the code; the intermediate branch is unstable. The preferred branch is very weakly modified by CRs. At high Mach numbers (≳10), the gas jump conditions approach that of a purely hydrodynamic shock, and a sub-grid prescription for thermal injection is required for reasonable acceleration efficiencies ${\sim}10{{\ \rm per\ cent}}$. CR-modified shocks have very long equilibration times (∼1000 diffusion time) required to develop the precursor, which must be resolved by ≳10 cells for convergence. Non-equilibrium effects, poor resolution, and obliquity of the magnetic field all reduce CR acceleration efficiency. Shocks in galaxy-scale simulations will generally contribute little to CR acceleration without sub-grid modification.
Rates and delay times of type Ia supernovae in the Dark Energy Survey
Authors: Wiseman P , Sullivan M , Smith M , Frohmaier C , Vincenzi M , Graur O , Popovic B , Armstrong P , Brout D , Davis T M , Galbany L , Hinton S R , Kelsey L , Kessler R , Lidman C , Möller A , Nichol R C , Rose B , Scolnic D , Toy M , Zontou Z , Asorey J , Carollo D , Glazebrook K , Lewis G F , Tucker B E , Abbott T M C , Aguena M , Allam S , Andrade-Oliveira F , Annis J , Bacon D , Bertin E , Brooks D , Buckley-Geer E , Burke D L , Rosell A Carnero , Kind M Carrasco , Carretero J , Costanzi M , da Costa L N , Pereira M E S , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Giannantonio T , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hollowood D L , Honscheid K , Hoyle B , James D J , Krause E , Kuehn K , Kuropatkin N , Maia M A G , Marshall J L , Martini P , Menanteau F , Miquel R , Morgan R , Ogando R L C , Palmese A , Paz-Chinchón F , Petravick D , Pieres A , Malagón A A Plazas , Romer A K , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , Thomas D , To C , Varga T N , Walker A R 
Published: July 2021

Abstract
We use a sample of 809 photometrically classified type Ia supernovae (SNe Ia) discovered by the Dark Energy Survey (DES) along with 40415 field galaxies to calculate the rate of SNe Ia per galaxy in the redshift range 0.2 &lt; z &lt; 0.6. We recover the known correlation between SN Ia rate and galaxy stellar mass across a broad range of scales 8.5 ≤ log (M*/M⊙) ≤ 11.25. We find that the SN Ia rate increases with stellar mass as a power-law with index 0.63 ± 0.02, which is consistent with previous work. We use an empirical model of stellar mass assembly to estimate the average star-formation histories (SFHs) of galaxies across the stellar mass range of our measurement. Combining the modelled SFHs with the SN Ia rates to estimate constraints on the SN Ia delay time distribution (DTD), we find the data are fit well by a power-law DTD with slope index β = −1.13 ± 0.05 and normalisation A = 2.11 ± 0.05 × 10−13SNeM⊙−1yr−1,, which corresponds to an overall SN Ia production efficiency $N_{\mathrm{Ia}}/M_* = 0.9 _{-0.7}^{+4.0} \times 10^{-3} \mathrm{SNe} \mathrm{M}_{\odot }^{-1}$,. Upon splitting the SN sample by properties of the light curves, we find a strong dependence on DTD slope with the SN decline rate, with slower-declining SNe exhibiting a steeper DTD slope. We interpret this as a result of a relationship between intrinsic luminosity and progenitor age, and explore the implications of the result in the context of SN Ia progenitors.
Growth of aggregates with liquid-like ice shells in protoplanetary discs
Authors: Musiolik Grzegorz 
Published: July 2021

ABSTRACT
During the first stages of planet formation, the collision growth of dust aggregates in protoplanetary discs (PPDs) is interrupted at the bouncing barrier. Dust aggregates coated by different species of ice turn out to be helpful to shift the bouncing barrier towards larger sizes due to their enhanced sticking properties in some cases. A rarely noticed fact is that H2O ice and H2O–CH3OH–NH3 ice behave liquid-like when UV irradiated within a PPD-similar environment. Dust aggregates coated by these ice species might be damped in collisions due to the liquid-like ice shell, which would effectively result in an increase of the sticking velocity. In this work, collisions of dust aggregates covered by the liquid-like H2O–CH3OH–NH3 ice shell are considered numerically. The coefficient of restitution and the sticking velocity are calculated for different thicknesses of the ice shell. The simulation predicts that an ice-shell thickness of few microns would be sufficient to allow the growth of cm-sized clusters in the PPD.
Deterrence and Self-Defence
Authors: Elzein Nadine 
Published: July 2021

Abstract
Measures aimed at general deterrence are often thought to be problematic on the basis that they violate the Kantian prohibition against sacrificing the interests of some as a means of securing a greater good. But even if this looks like a weak objection because deterrence can be justified as a form of societal self-defence, such measures may be regarded as problematic for another reason: Harming in self-defence is only justified when it’s necessary, i.e., when there are no relatively harmless alternatives. While there are few harmless ways to remove the threat posed by dangerous individuals, there are many relatively harmless methods for preventing crime. We can bracket off our preventative failings when we think of present threats, but we cannot do so when contemplating alternative preventative measures.
Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
Authors: Bayne Rosemary A , Jayachandran Uma , Kasprowicz Aleksandra , Bresson Stefan , Tollervey David , Wallace Edward W J , Cook Atlanta G 
Published: July 2021

Abstract
Ssd1, a conserved fungal RNA-binding protein, is important in stress responses, cell division and virulence. Ssd1 is closely related to Dis3L2 of the RNase II family of nucleases, but lacks catalytic activity and likely suppresses translation of bound mRNAs. Previous studies identified RNA motifs enriched in Ssd1-associated transcripts, yet the sequence requirements for Ssd1 binding are not defined. Here, we identify precise binding sites of Ssd1 on RNA using in vivo cross-linking and cDNA analysis. These sites are enriched in 5′ untranslated regions of a subset of mRNAs encoding cell wall proteins. We identified a conserved bipartite motif that binds Ssd1 with high affinity in vitro. Active RNase II enzymes have a characteristic, internal RNA binding path; the Ssd1 crystal structure at 1.9 Å resolution shows that remnants of regulatory sequences block this path. Instead, RNA binding activity has relocated to a conserved patch on the surface of the protein. Structure-guided mutations of this surface prevent Ssd1 from binding RNA in vitro and phenocopy Ssd1 deletion in vivo. These studies provide a new framework for understanding the function of a pleiotropic post-transcriptional regulator of gene expression and give insights into the evolution of regulatory and binding elements in the RNase II family.
TB or not to be: what specificities and impact do antibodies have during tuberculosis?
Authors: Hermann Clemens , King Carolyn G 
Published: July 2021

Abstract
Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis (Mtb), is a major cause of global morbidity and mortality. The primary barrier to the development of an effective tuberculosis vaccine is our failure to fully understand the fundamental characteristics of a protective immune response. There is an increasing evidence that mobilization of antibody and B cell responses during natural Mtb infection and vaccination play a role in host protection. Several studies have assessed the levels of Mtb-specific antibodies induced during active disease as well as the potential of monoclonal antibodies to modulate bacterial growth in vitro and in vivo. A major limitation of these studies, however, is that the specific antigens capable of eliciting humoral responses are largely unknown. As a result, information about antibody dynamics and function, which might fundamentally transform our understanding of host Mtb immunity, is missing. Importantly, Mtb infection also induces the recruitment, accumulation and colocalization of B and T cells in the lung, which are positively correlated with protection in humans and animal models of disease. These ectopic lymphoid tissues generally support local germinal center reactions for the proliferation and ongoing selection of effector and memory B cells in the mucosa. Efforts to leverage such responses for human health, however, require a more complete understanding of how antibodies and B cells contribute to the local and systemic host Mtb immunity.
Entering a new academic year: the problem faced in online learning amid COVID-19 pandemic
Authors: Rosales Renniel Jayson Jacinto , Pagsuyoin Juan Carlos C 
Published: July 2021

Abstract
In the crisis, we are facing, the well-being of the students is given importance in their online learning. Attention has already been given as to how the school may support in making the parents mentally healthy as they assist their children in learning. The Philippines is already entering another online academic school year as part of the health and safety protocol during this pandemic. But with all the challenges experienced by the stakeholders, the education sector is also facing a problem as to the well-being of the teachers who are also struggling in this pandemic with all the changes in their routines since online learning began.
Improving outcomes for patients hospitalized with gout: a systematic review
Authors: Russell Mark D , Clarke Benjamin D , Roddy Edward , Galloway James B 
Published: July 2021

Abstract

Objectives
Hospital admissions for gout flares have increased dramatically in recent years, despite widely available, effective medications for the treatment and prevention of flares. We conducted a systematic review to evaluate the effectiveness and implementation of interventions in patients hospitalized for gout flares.

Methods
A search was conducted in MEDLINE, Embase and the Cochrane library, from database inception to 8 April 2021, using the terms ‘gout’ and ‘hospital’ and their synonyms. Studies were included if they evaluated the effectiveness and/or implementation of interventions during hospital admissions or emergency department attendances for gout flares. Risk of bias assessments were performed for included studies.

Results
Nineteen articles were included. Most studies were small, retrospective analyses performed in single centres, with concerns for bias. Eleven studies (including five randomized controlled trials) reported improved patient outcomes following pharmacological interventions with known efficacy in gout, including allopurinol, prednisolone, NSAIDs and anakinra. Eight studies reported improved outcomes associated with non-pharmacological interventions: inpatient rheumatology consultation and a hospital gout management protocol. No studies to date have prospectively evaluated strategies designed to prevent re-admissions of patients hospitalized for gout flares.

Conclusion
There is an urgent need for high-quality, prospective studies of strategies for improving uptake of urate-lowering therapies in hospitalized patients, incorporating prophylaxis against flares and treat-to-target optimization of serum urate levels. Such studies are essential if the epidemic of hospital admissions from this treatable condition is to be countered.
Updates on interferon in juvenile dermatomyositis: pathogenesis and therapy
Authors: Kim Hanna 
Published: July 2021

Purpose of review
This review provides updates regarding the role of interferon (IFN) in juvenile dermatomyositis (JDM), including comparison to interferonopathies and therapeutic implications.

Recent findings
Transcriptomic and protein-based studies in different tissues and peripheral IFN-α assessment have demonstrated the importance of the dysregulated IFN pathway in JDM. Additional studies have validated IFN-regulated gene and protein expression correlation with disease activity in blood and muscle, with potential to predict flares. Type I and II IFN both are dysregulated in peripheral blood and muscle, with more type I IFN in skin. Muscle studies connects hypoxia to IFN production and IFN to vascular dysfunction and muscle atrophy. JDM overlaps with interferonopathy phenotype and IFN signature. There are multiple case reports and case series noting decreased IFN markers and clinical improvement in refractory JDM with Janus kinase (JAK) inhibitors.

Summary
Studies confirm IFN, particularly type I and II IFN, is an important part of JDM pathogenesis by the level of dysregulation and correlation with disease activity, as well as IFN recapitulating key JDM muscle pathology. Smaller studies indicate there may be differences by myositis-specific autoantibody group, but validation is needed. JAK inhibitors are a promising therapy as they can inhibit IFN signaling, but further study is needed regarding which patients will benefit, dosing, and safety monitoring.
Esophageal Perforation After Anterior Cervical Surgery
Authors: Modi Hitesh N. , Shreshtha Utsab , Patel Udit , Kotecha Hardik , Patel Mahesh D. , Dileep Pratibha 
Published: July 2021

Summary and Background:Esophageal perforation (EP) after anterior cervical surgery is a rare but potentially life-threatening condition. EP caused by malpositioned implants in cervical spine injury with multiple comorbidities is challenging to treat simultaneously.Study:This was a case report study.Purpose of Study:The aim of this study was to present successful treatment of EP in a subluxated C5–C6 level with implant failure, infection, septicemia, and comorbidities. The aim was to emphasize the need for a multispecialty approach while treating serious complications.Case:A 72-year-old woman presented to the ER with a history of operated cervical spine a week ago and having breathlessness, fever, wound infection, and tracheostomy in situ. After primary investigations, the patient was initially treated in the intensive care unit, where bleeding from the tracheostomy site was noticed. Upon endoscopy, EP was diagnosed due to implant failure. She was operated for revision cervical spine surgery (drainage of pus with anterior and posterior cervical fixation) and percutaneous endoscopic gastrostomy tube insertion (esophageal diversion). On exploration of EP, a decision was made to perform conservative treatment as initial tag sutures did not hold due to infection. Postoperatively, the patient developed rectal bleed 3 times, which was ultimately treated with cecal bleed embolization. The infected cervical wound was managed with an open dressing. The patient was managed with intermittent assisted ventilation through tracheostomy postoperatively. Barium swallow at 10 weeks confirmed healing of EP and oral feed was started. Tracheostomy closure was performed once the wound had healed, and the patient was discharged with improved neurology at 12 weeks.Conclusions:Perioperative problems after cervical surgery such as breathing difficulty, wound discharge, and worsening of neurology may lead to suspicion of underlying EP due to implant failure. Upper gastrointestinal endoscopy needs to be considered for a prompt diagnosis. Revision spine surgery with treatment of perforation simultaneously and maintenance of enteral nutrition through a percutaneous endoscopic gastrostomy tube with a multispecialty approach is recommended for this potentially life-threatening condition.
Large Plaque-type Blue Nevus with GNAQ Q209P Mutation, Involving Mammary Gland Tissue: Under-Recognized Mammary Condition as an Origin of Primary Mammary Melanocytic Tumors
Authors: Satake Kosuke , Sudo Tamotsu , Sugino Takashi , Yoshikawa Shusuke , Kiyohara Yoshio , Hayashi Tomomi , Nakashima Kazuaki , Goto Keisuke 
Published: July 2021

Abstract:Plaque-type blue nevus is a rare variant of blue nevi that was first described in 1954. This article presents clinical, macroscopic, histopathological, and genetic findings for a case of large plaque-type blue nevus expanding into the mammary gland tissue as well as the skin of the right breast. A 63-year-old woman presented with a congenital, large, blue-colored macule limited to the hypochondriac area of the right breast. A nodule 8 mm in diameter was also present in the mammary gland tissue. Magnetic resonance imaging was unable to detect diffuse melanin deposition in the mammary gland tissue, but pigmentation in the whole mammary parenchyma was observed in the cut surfaces of the mastectomy specimen. Histopathology revealed a sparse distribution of dendritic melanocytes in whole sections of the mammary fibrous tissue and partial sections of the dermis. The histopathological criteria for atypical cellular blue nevus were fulfilled for the mammary tumor. Nodal blue nevus was diagnosed in the sentinel lymph node. Sanger sequencing confirmed theGNAQQ209P mutation, which was also identified in all 4 literature cases of plaque-type blue nevus, but rarely in conventional blue nevi and uveal melanoma. It should be noted that plaque-type blue nevus can expand into the mammary gland tissue, even if the pigmented lesion does not exist on the overlying breast skin. The mammary condition can be the origin of primary mammary melanocytic tumors. Mosaicism of theGNAQQ209P mutation can be a characteristic genetic alteration to extensive blue nevi, including plaque-type blue nevus.
Optimizing Detection of Lymphatic Invasion in Primary Cutaneous Melanoma With the Use of D2-40 and a Paired Melanocytic Marker
Authors: Straker Richard J. , Taylor Laura A. , Neuwirth Madalyn G. , Sinnamon Andrew J. , Shannon Adrienne B. , Abbott James , Miura John T. , Chu Emily Y. , Xu Xiaowei , Karakousis Giorgos C. 
Published: July 2021

Abstract:
Dual immunohistochemical (IHC) staining with D2-40 and S100 improves detection of lymphatic invasion (LI) in primary cutaneous melanoma. However, limited data exist evaluating this technique using other melanocytic markers, and thus, the optimal marker for detection of LI is unestablished. To address this knowledge gap, a case–control study was performed comparing melanoma specimens from 22 patients with known lymphatic spread (LS) with a control group of 11 patients without LS. Specimens underwent dual IHC staining with D2-40 and MART-1, SOX-10, and S100 to evaluate for LI. Receiver operating characteristic analysis was used to estimate each stain's accuracy for detection of LI. The LS group was more likely to be ≥65 years (P = 0.04), have a tumor thickness of ≥1 mm (P < 0.01), and have ulcerated tumors (P = 0.02). Detection of LI with D2-40/MART-1 significantly correlated with LS (P = 0.03), and the D2-40/MART-1 stain was most accurate for LI based on receiver operating characteristic curve analysis (area under the curve [AUC] 0.705) in comparison with D2-40/SOX-10 (AUC 0.575) and D2-40/S100 (AUC 0.633). These findings suggest that MART-1 may be the optimal melanocytic marker to combine with D2-40 for detection of LI in melanoma. Further studies are needed to determine the utility of routinely performing these stains for histopathologic analysis of melanoma.
Unusual Presentation of Extensor Tendon Rupture Caused by a Dorsal Wrist Synovial Cyst
Authors: Allahham Salim , Aljassem Ghanem , Alyazji Zaki , Sada Ruba , Abuelgasim Mutaz , Otman Sami , Albasti Habib 
Published: July 2021

Summary:
Synovial cysts are juxta-articular-fluid–filled collections that are lined by synovial cells, distinguishing them from a very close cystic lesion, which is the ganglion cyst. They usually present with pain and unpleasant appearance; here we present a case of wrist synovial cyst that caused extensor tendon rupture. A 50-year-old woman presented to our clinic with a cystic lesion on the dorsum of her wrist, with an inability to extend her index finger. The lesion was found intraoperatively engulfing the extensors of the index and causing a rupture. The cyst was excised and the tendon was reconstructed; pathology report confirmed the lesion as synovial cyst. Synovial cysts and ganglion cysts are two different entities but they have been used interchangeably in the literature; pathology is the only way to differentiate between them because they usually present with identical scenarios. None of them were reported to cause extensor tendon rupture, as presented in our article. Synovial cysts can cause rupture to extensor tendons if they arise from the sheath, and it is better to anticipate synovial cyst and remove it surgically before causing any further damage, if the lesion appeared to rise from the tendon sheath on further imaging.
Gaps in standards for integrating artificial intelligence technologies into ophthalmic practice
Authors: Baxter Sally L. , Lee Aaron Y. 
Published: July 2021

Purpose of review
The purpose of this review is to provide an overview of healthcare standards and their relevance to multiple ophthalmic workflows, with a specific emphasis on describing gaps in standards development needed for improved integration of artificial intelligence technologies into ophthalmic practice.

Recent findings
Healthcare standards are an essential component of data exchange and critical for clinical practice, research, and public health surveillance activities. Standards enable interoperability between clinical information systems, healthcare information exchange between institutions, and clinical decision support in a complex health information technology ecosystem. There are several gaps in standards in ophthalmology, including relatively low adoption of imaging standards, lack of use cases for integrating apps providing artificial intelligence -based decision support, lack of common data models to harmonize big data repositories, and no standards regarding interfaces and algorithmic outputs.

Summary
These gaps in standards represent opportunities for future work to develop improved data flow between various elements of the digital health ecosystem. This will enable more widespread adoption and integration of artificial intelligence-based tools into clinical practice. Engagement and support from the ophthalmology community for standards development will be important for advancing this work.