bluuebunny/crossref_metadata_2025_split huggingface dataset:
A parallel sampling algorithm for some nonlinear inverse problems
Authors: Volkov Darko 
Published: January 2022

AbstractWe derive a parallel sampling algorithm for computational inverse problems that present an unknown linear forcing term and a vector of nonlinear parameters to be recovered. It is assumed that the data are noisy and that the linear part of the problem is ill-posed. The vector of nonlinear parameters ${m} $ is modeled as a random variable. A dilation parameter $\alpha $ is used to scale the regularity of the linear unknown and is also modeled as a random variable. A posterior probability distribution for $({m}, \alpha )$ is derived following an approach related to the maximum likelihood (ML) regularization parameter selection (Galatsanos, N. P. & Katsaggelos, A. K. (1992). Methods for choosing the regularization parameter and estimating the noise variance in image restoration and their relation. IEEE Trans. Image Process., 1, 322–336). A major difference in our approach is that, unlike in Galatsanos, N. P. & Katsaggelos, A. K. (1992, Methods for choosing the regularization parameter and estimating the noise variance in image restoration and their relation. IEEE Trans. Image Process., 1, 322–336), we do not limit ourselves to the maximum likelihood value of $\alpha $. We then derive a parallel sampling algorithm where we alternate computing proposals in parallel and combining proposals to accept or reject them as in Calderhead, B. (2014, A general construction for parallelizing metropolis- hastings algorithms. Proc. Natl Acad Sci, 111, 17408–17413). This algorithm is well suited to problems where proposals are expensive to compute. We then apply it to an inverse problem in seismology. We show how our results compare favorably to those obtained from the ML, the Generalized Cross Validation and the Constrained Least Squares algorithms.
Acute appendicitis during the COVID-19 pandemic—changes in incidence and clinical presentation but not in patients’ outcome
Authors: Wolf Sebastian , Schrempf Matthias , Vlasenko Dmytro , Schoeler Claus , Erckmann Frank , Von Parpart Patrick , Paschwitz Rieke , Anthuber Matthias , Sommer Florian 
Published: January 2022

Abstract

Background
The coronavirus disease 2019 (COVID-19) pandemic is an ongoing severe issue.

Objective
The aim of this study was to compare the incidence, severity and treatment of acute appendicitis (AA) before and during the COVID-19 pandemic.

Methods
A retrospective cohort analysis was conducted between January 2019 and April 2020 in one high-volume center. A comparison was performed between two groups (Group A: patients admitted with AA before the COVID-19 pandemic; Group B: patients admitted with AA at the beginning of the pandemic) in terms of the incidence of AA and clinical and pathological outcomes. The incidence of AA was also analyzed in six surrounding peripheral hospitals.

Results
A total of 94 patients were identified, 54 in Group A and 40 in Group B (57% vs. 43%). Demographic data were comparable between groups. AA in Group B showed a significant higher rate of histological advanced cases (10 (18.5%) Group A vs. 20 (50%) Group B, P = 0.001) and the need for postoperative antibiotic treatment (6 (11.1%) Group A vs. 11 (27.5%) Group B, P = 0.045). During the pandemic, a higher percentage of patients were treated at peripheral hospitals (Group A: 54/111 vs. 40/126).

Conclusion
During the onset of the COVID-19 pandemic there was a significant decrease of patients with AA in a high-volume center, which showed more advanced disease of AA. This significant decrease in the high-volume center correlates with an increase in patients with AA in peripheral hospitals and represents a change in patient flow during the onset of the pandemic.
Strategic Cruelty: Legitimizing Violence in the European Union's Border Regime
Authors: Sajjad Tazreena 
Published: January 2022

AbstractViolent border practices against irregular migration are not new, although increasing xenophobia and anti-immigrant sentiments have drawn greater attention to such practices in recent years. Such measures—both in and at the borders—constitute organized violence on migrant bodies, making them permanently insecure. This is particularly striking in the context of European liberal democracies with its established discourse of human rights, which have since the 1990s consolidated a formidable architecture of deterrence and which have intensified such efforts with the 2015 “migrant crisis” with increasing sea interceptions, restrictive anti-immigrant measures, and the criminalization of solidarity efforts. This article asks: How does the European Union (EU) legitimize violence in its border regime and reconcile this regime with its core identity as a defender of human rights and a “normative superpower”? By drawing on critical discourse analysis and reviewing policy statements, speeches, and press releases, it identifies the discourse topics, discursive strategies, and linguistic means through which EU migration discourse seeks to legitimize its sprawling architecture of strategic cruelty against irregular migration. This article argues that the purpose of the resulting discourse is to “absolve and resolve”—absolving the union as a whole of guilt and resolving the cognitive dissonance between the professed identity of the EU as supremely humanitarian and the observable inhumane acts of itself and its member states. This explains how the EU can employ strategic cruelty to mitigate the arrival of migrants while simultaneously maintaining moral standing to chastise individual members for “violating” the hegemonic collective identity of the union.
The complete mitochondrial genome of the spot prawn,Pandalus platycerosBrandt in von Middendorf, 1851 (Decapoda: Caridea: Pandalidae), assembled from linked-reads sequencing
Authors: Cronin Timothy J , Jones Steven J M , Baeza J Antonio 
Published: January 2022

AbstractPandalus platyceros Brandt in von Middendorf, 1851, the spot prawn, is a commercially important pandalid shrimp that sustains a small fishery in the northeastern Pacific Ocean. We report, for the first time, the complete mitochondrial genome of P. platyceros, while also testing whether linked-reads sequencing (10X Genomics) data can be used to assemble complete and accurate mitochondrial genomes. The pipeline GetOrganelle assembled and circularized the complete mitochondrial chromosome of P. platyceros with an average coverage of 28.2x from a dataset of 5 M pairs of linked reads. The AT-rich mitochondrial genome of P. platyceros is 16,628 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 24 transfer RNA genes. One copy of all tRNA genes was present, except for tRNA-G, which had three copies. A single 1,077 bp-long intergenic space was assumed to be the D-loop/Control region. Selective pressure analysis indicated the PCGs were under purifying selection, although levels differed among genes. The highest KA:KS ratios were found in nad4 and nad4l, suggesting weaker purifying selection and environmental constraints on these genes. The KA:KS ratios for cob and cox1 were a magnitude lower than the ratios in other PCGs, suggesting strong purifying selection acting upon these genes. A maximum likelihood phylogenetic analysis based on all PCGs that included a total of 91 species of shrimps supported the monophyly of the infraorder Caridea and family Pandalidae. Furthermore, the monophyly of other caridean families, including Alvinocaridae, Atyidae, Thoridae, Lysmatidae, and Palaemonidae was also supported by the same analysis. Our results thus suggest that mitochondrial PCGs have enough phylogenetic information to resolve relationships at high taxonomic levels (families) in Caridea. This study contributes new genomic resources for this commercially important species and demonstrates that linked-reads sequencing can be used to assemble accurate mitochondrial genomes.
The complete mitochondrial genome of the Atlantic ghost crabOcypode quadrata(Fabricius, 1787) (Brachyura: Ocypodidae: Ocypodinae)
Authors: O’Brien Connor , Bracken-Grissom Heather D , Baeza J Antonio 
Published: January 2022

AbstractThe semi-terrestrial Atlantic ghost crab Ocypode quadrata (Fabricius, 1787) is a medium-sized species that inhabits the supralittoral zone in sandy temperate and tropical beaches of the western Atlantic Ocean. Despite the relevant ecological role of O. quadrata and its use as a bio-indicator, there are currently few genetic and genomic resources for this species. This study assembled and characterized in detail the complete mitochondrial genome of O. quadrata from Illumina short paired-end reads. The software NOVOplasty assembled and circularized the complete mitochondrial genome of the Atlantic ghost crab with an average coverage of 162×, per nucleotide. The AT-rich mitochondrial genome of O. quadrata is 15,547 bp in length, consisting of 13 protein coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes (rrnL and rrnS). A single 685 bp long non-coding nucleotide region is assumed to be the D-loop/control region. The observed gene order in O. quadrata is identical to that reported for all congeneric species with known mitochondrial genomes. A selective pressure analysis indicates that all the PCGs are under purifying selection. Differences in KA/KS ratios among genes indicate strong purifying selection in the cox1, cox2, cox3, and atp6 genes, and weaker purifying selection in the atp8 gene. The 22 tRNA genes range from 64 to 70 bp in length, and all the tRNAs show a conventional “cloverleaf” secondary structure except for trnS1 that is missing the D-arm, in agreement to that reported for other brachyuran crabs with tRNA secondary depictions published. A maximum likelihood phylogenetic analysis based on all PCGs that included a total of 18 species of crabs fully supported the monophyly of the family Ocypodidae. The monophyly of the subfamilies Ocypodinae and Ucinidae was also highly supported by the analysis. These results suggest that mitochondrial PCGs have “phylogenetic signal” to reveal natural relationships at high taxonomic levels in crabs belonging to the family Ocypodidae. This study represents a new genomic resource for this ecologically relevant bioindicator ghost crab.
‘I shall now go on selling as much as I can to these people’
Authors: Davoli Silvia 
Published: January 2022

Abstract
This article reassesses the collecting activities of Herbert Stern (1851–1919), 1st Baron Michelham, and his wife, Geraldine (1882–1927), at the start of the twentieth century, when their lives were lived partly in France and partly in Britain. The first section provides a general overview of the Stern family and their social, cultural and philanthropic activities, which were comparable in scope and range with those of other German–Jewish families established in the United Kingdom at the time. The later sections outline their progressive detachment from this model in favour of a decidedly cosmopolitan direction, a transformation initiated by Lord and Lady Michelham and completed with the assistance of the Jewish art dealer Joseph Duveen.
Effects of Irradiated Sterile Male and Mating Sequence on the Fertility of Drosophila suzukii (Diptera: Drosophilidae)
Authors: Chen Yongzhuo , Pan Hui , Li Jing , Pan Deng , Liu Pengcheng , Hu Haoyuan 
Published: January 2022

Abstract
The sterile insect technique has been explored in the laboratory to control populations of Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), a globally invasive pest. We studied the reproductive behavior of D. suzukii including mating frequency, time between matings, and mating duration among non-irradiated flies. Irradiation doses were tested at 0, 60, 90, 110, 120, 150, and 180 Gy to select the optimal dose for producing sterile males. In addition, we examined the effects of mating sequence on offspring production where females were presented with irradiated males first and then wild males, or the reverse. Female D. suzukii were found to mate twice on average through their lifespan, with 16.53 ± 12.05 d between matings. The first mating duration was 24.64 ± 1.52 min shorter than the second mating. A dose of 90 Gy was suitable where irradiated males lived as long as non-irradiated males, and few eggs hatched from matings. The mating sequence experiment revealed first-male parentage preference. Wild females that mated with a wild male and then irradiated male produced more offspring than females mated with an irradiated and then wild male. Overall, the influence of mating sequence should be taken into consideration when applying the sterile insect technique (SIT) to control D. suzukii populations.
Altered Mental Status After Hematopoietic Stem Cell Transplant
Authors: Failing Jarrett J. , Abu Saleh Omar M. , Whitaker Jennifer A. 
Published: January 2022

Abstract
Human herpesvirus (HHV) 6 is a member of the Betaherpesvirinae family. There are 2 species of the virus, HHV-6A and HHV-6B, but most infections in allogeneic hematopoietic stem cell transplant patients are due to HHV-6B. Risk factors for activating a latent HHV-6 infection include severe immunosuppression, umbilical cord blood transplant, bone marrow transplant with an unrelated donor, and corticosteroid treatment. Symptoms include memory loss (classically anterograde amnesia), confusion, delirium, and loss of consciousness. The recommended first-line agents for treatment of HHV-6 encephalitis are ganciclovir or foscarnet for 3 to 6 weeks.
Premature Closure
Authors: Challener Douglas W. , Marcelin Jasmine R. , Tande Aaron J. 
Published: January 2022

Abstract
Shortcuts in clinical reasoning delay accurate diagnoses and result in inappropriate treatment. Psychologists have described these shortcuts as heuristics and have created a classification system for these errors. The defined heuristics include premature closure, anchoring bias, blind obedience, the availability heuristic, and framing effects. With greater knowledge of the common diagnostic pitfalls, physicians can attempt to avoid these errors.
The Other Coinfection
Authors: Tan Eugene M. , Marcelin Jasmine R. , Rizza Stacey A. 
Published: January 2022

Abstract
Patients may have an acute hepatitis B virus (HBV) and hepatitis D virus (HDV) coinfection from concurrent transmission, or they may have HDV superinfection of a chronic HBV infection. HBV and HDV coinfection can present as a mild, self-limited infection, but it may progress to fulminant hepatitis or cirrhosis for 20% of patients. Patients with an HDV superinfection of a chronic HBV infection can present with acute hepatitis or exacerbation of an existing liver disease. To diagnose HDV infection, all patients with positive test results for hepatitis B surface antigen should undergo testing for anti-HDV immunoglobulin G or total antibodies. Treatment goals include suppressing replication of HDV and HBV. To tailor antimicrobial activity against HDV, an HBV treatment regimen could include weekly standard or pegylated interferon-alfa for 12 to 18 months.
An Earache Too Far
Authors: Esquer-Garrigos Zerelda , Marcelin Jasmine R. , Hernandez-Acosta Alfonso , Sampathkumar Priya 
Published: January 2022

Abstract
Despite the development of effective systemic antibiotic therapy, bacterial meningitis continues to be a significant cause of morbidity and mortality in the United States. Numerous studies of different populations report that Steptococcus pneumoniae is the species most commonly involved in bacterial meningitis cases. The prevalence of S pneumoniae in bacterial meningitis can range from 50% to 70%, and incidence rates increase with age. In recent years, pneumococcal vaccination has decreased the incidence of meningitis cases caused by the serotypes included in the vaccine. The current recommended treatment for suspected pneumococcal meningitis is vancomycin plus a third-generation cephalosporin until susceptibilities are determined.
Not So Good
Authors: Challener Douglas W. , Marcelin Jasmine R. 
Published: January 2022

Abstract
Good syndrome (GS) is a hypogammaglobulinemia associated with the presence of a thymoma. Patients with GS often are adults who present with recurrent upper respiratory tract infections and anterior mediastinal masses. GS has no formal diagnostic criteria. The syndrome is defined most commonly as a thymoma plus humoral and cellular immune deficiency. The cause of GS is not known. The primary clinical manifestations of GS are caused by the immunodeficiency. Patients with GS are susceptible to a wide range of infections. Treatment of GS consists of thymectomy and immunoglobulin replacement with intravenous immunoglobulin.
A Little Atypical
Authors: Vijayvargiya Prakhar , Marcelin Jasmine R. , Esquer-Garrigos Zerelda , Whitaker Jennifer A. 
Published: January 2022

Abstract
Legionnaires disease (LD) is caused by an intracellular gram-negative bacillus of the genus Legionella. Human infection occurs via inhalation of infectious aerosols. Fever with pulse-temperature dissociation, diarrhea, nonproductive cough, and confusion can indicate LD. The preferred method for diagnosis is to perform both a urine antigen test and a sputum culture. Levofloxacin and azithromycin are the antibiotics that are most active against LD. The usual antibiotic course lasts for 7 to 10 days, with up to 21 days of therapy recommended for immunocompromised patients. LD is noncontagious and person-to-person transmission does not occur.
Thrombocytopenia
Authors: Abeykoon Jithma P. , Abu Saleh Omar M. , Rivera Candido E. 
Published: January 2022

Abstract
Drug-induced thrombocytopenia (DITP) is commonly attributed to antimicrobial agents; 153 drugs are believed to have a high probability of causing immune-mediated thrombocytopenia. Rifampin is categorized as a definite cause of DITP. Median time to presentation with thrombocytopenia after rifampin exposure is 1 to 2 weeks. DITP in current medical practice largely remains a clinical diagnosis. The therapy for DITP is discontinuation of the offending agent. Although DITP is associated with a high incidence of morbidity and mortality, the possibility of completely reversing it by discontinuing the offending agent indicates that an accurate and timely diagnosis is vital.
Ulcerative Skin Lesions in a Returned Traveler
Authors: Fida Madiha , Tan Eugene M. , Enzler Mark J. 
Published: January 2022

Abstract
Cutaneous leishmaniasis (CL) may present as a disseminated infection (visceral) or with lesions involving the skin or oral or nasal mucosa. Leishmaniasis is transmitted by the bite of infected sand flies. Diagnosis of CL is made by histopathologic observation of the amastigote form of the parasite, by parasite cultures, or by molecular methods. In immunocompetent individuals, infection may resolve without treatment. Therapeutic options include cryotherapy, thermotherapy, and photodynamic therapy or topical paromomycin. Preventive strategies include individual protective measures such as minimizing exposed skin, using bed nets, applying insect repellents to bare skin, and wearing permethrin-treated clothing.
A Chronic Polyarthritis
Authors: Challener Douglas W. , Marcelin Jasmine R. , Cawcutt Kelly A. 
Published: January 2022

Abstract
Whipple disease (WD) is a rare, systemic illness characterized by weight loss, diarrhea, abdominal pain, and arthralgias. Common features at presentation are colicky abdominal pain and watery diarrhea that lead to weight loss, plus arthralgia and arthritis. Diagnosis is often established with small-bowel examination and biopsy. WD usually is curable, but successful treatment requires prolonged courses of antibiotics. Effective treatment of long-term classical or localized WD consists of induction therapy with intravenous ceftriaxone or penicillin G for 2 weeks, followed by 1 year of maintenance therapy with trimethoprim-sulfamethoxazole.
Detection of anti-Histoplasma capsulatum antibodies and seroconversion patterns in critically ill patients with COVID-19: An underdiagnosed fungal entity complicating COVID-19?
Authors: Toscanini María A , Barberis Fernanda , Benedetti María F , Garrido Agustín Videla , Posse Gladys B , Capece Paula , Daneri Gabriela López , Nusblat Alejandro D , Cuestas María L 
Published: January 2022

Abstract

The patients with severe COVID-19 are at increased risk for invasive fungal infections, such as invasive pulmonary aspergillosis and candidiasis, which increase morbidity and mortality. However, clinicians should also consider the possibility of reactivating latent Histoplasma capsulatum in patients with severe COVID-19 living within areas of endemicity who have worsening respiratory function or sepsis, even if they do not have classical risk factors for histoplasmosis (e.g., HIV/AIDS). Bearing in mind this scenario, serum samples of 39 non-HIV/AIDS patients from Buenos Aires hospitalized due to severe COVID-19 pneumonia were analyzed for anti-H. capsulatum-specific IgG antibodies by an in-house ELISA. Antibodies against H. capsulatum were detected in the sera of 8/39 patients (20.51%). To exclude the possibility that these antibodies arose from past exposure of these patients to the fungus, paired serum samples obtained after an interval of at least 10 days were evaluated. Of them, five patients (62.5%) with negative anti-H. capsulatum antibodies at baseline became seropositive 7–10 days later. Three patients (37.5%) had positive anti-H. capsulatum antibodies at baseline, but at time point 2, one of them became seronegative and the other one diminished the antibody titers (4000 vs. 16000 at baseline). The remaining patients displayed higher antibody titers at time point 2 (4000 vs. 1000 at baseline) and died immediately thereafter. In conclusion, awareness of the possibility of fungal co-infections is essential to reduce delays in diagnosis and treatment in order to help prevent severe illness and death from these infections.

Lay summary
This study verifies that patients with severe COVID-19 at ICU are at risk for histoplasmosis reactivation in endemic areas. Accurate diagnosis of this deadly fungal disease among critically ill patients with COVID-19 living in endemic areas for histoplasmosis is needed.
Study of timing and spectral properties of the X-ray pulsar 1A 0535+262 during the giant outburst in 2020 November–December
Authors: Mandal Manoj , Pal Sabyasachi 
Published: January 2022

ABSTRACT
We made a detailed study of the timing and spectral properties of the X-ray pulsar 1A 0535+262 during the recent giant outburst in 2020 November and December. The flux of the pulsar reached a record value of ∼12.5 Crab as observed by Swift/BAT (15–50 keV) and the corresponding mass accretion rate was ∼6.67 × 1017 g s−1 near the peak of the outburst. There was a transition from the subcritical to the supercritical accretion regime which allows exploring different properties of the source in the supercritical regime. A q-like feature was detected in the hardness–intensity diagram during the outburst. We observed high variability and strong energy dependence of pulse profiles during the outburst. Cyclotron Resonant Scattering Feature (CRSF) was detected at ∼44 keV from the NuSTAR energy spectrum in the subcritical regime and the corresponding magnetic field was B ≃ 4.9 × 1012 G. The energy of the CRSF was shifted towards lower energy in the supercritical regime. The luminosity dependence of the CRSF was studied and during the supercritical regime, a negative correlation was observed between the line energy and luminosity. The critical luminosity was ∼6 × 1037erg s−1 above which a state transition occurred. A reversal of correlation between the photon index and luminosity was observed near the critical luminosity. The NuSTAR spectra can be described by a composite model with two continuum components, a blackbody emission, cut-off power law, and a discrete component to account for the iron emission line at 6.4 keV. An additional cyclotron absorption feature was included in the model.