bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism
Authors: Schwedt Inge , Collignon Madeline , Mittelstädt Carolin , Giudici Florian , Rapp Johanna , Meißner Janek , Link Hannes , Hertel Robert , Commichau Fabian M. 
Published: June 2023

AbstractGlyphosate (GS) specifically inhibits the 5‐enolpyruvyl‐shikimate‐3‐phosphate (EPSP) synthase that converts phosphoenolpyruvate (PEP) and shikimate‐3‐phosphate to EPSP in the shikimate pathway of bacteria and other organisms. The inhibition of the EPSP synthase depletes the cell of the EPSP‐derived aromatic amino acids as well as of folate and quinones. A variety of mechanisms (e.g., EPSP synthase modification) has been described that confer GS resistance to bacteria. Here, we show that the Burkholderia anthina strain DSM 16086 quickly evolves GS resistance by the acquisition of mutations in the ppsR gene. ppsR codes for the pyruvate/ortho‐Pi dikinase PpsR that physically interacts and regulates the activity of the PEP synthetase PpsA. The mutational inactivation of ppsR causes an increase in the cellular PEP concentration, thereby abolishing the inhibition of the EPSP synthase by GS that competes with PEP for binding to the enzyme. Since the overexpression of the Escherichia coli ppsA gene in Bacillus subtilis and E. coli did not increase GS resistance in these organisms, the mutational inactivation of the ppsR gene resulting in PpsA overactivity is a GS resistance mechanism that is probably unique to B. anthina.
Long‐term stability of pleural fluid carcinoembryonic antigen and its effect on the diagnostic accuracy for malignant pleural effusion
Authors: Yang Dan‐Ni , Niu Yan , Wen Jian‐Xun , Wen Xu‐Hui , Wang Ya‐Fei , Yan Li , Jiang Ting‐Wang , Huang Jin‐Hong , Chen Hong , Lippi Giuseppe , Zheng Wen‐Qi , Hu Zhi‐De 
Published: June 2023

AbstractBackgroundThe in vitro stability assessment is essential for investigating the diagnostic accuracy of pleural biomarkers. This study aimed to investigate the long‐term stability of pleural fluid carcinoembryonic antigen (CEA) at −80°C to −70°C. In addition, we analyzed the effects of frozen storage on the diagnostic accuracy of CEA for malignant pleural effusion (MPE).MethodsPleural fluid CEA of participants in two prospective cohorts were stored at −80°C to −70°C for 1–3 years. The CEA level in the stored specimen was measured with an immunoassay, and its level in the fresh specimen was extracted from medical records. The Bland–Altman method, Passing‐Bablok regression, and Deming regression were used to analyze the agreement of CEA between the fresh and frozen pleural fluid. In addition, we used receiver operating characteristic (ROC) curves to evaluate the diagnostic accuracy of CEA in the fresh and frozen specimens for MPE.ResultsA total of 210 participants were enrolled. The median CEA levels in frozen and fresh pleural fluid specimens were similar (frozen, 2.32 ng/mL; fresh, 2.59 ng/mL; p < 0.01). The slopes and intercepts in the Passing‐Bablok regression (intercept 0.01, slope 1.04) and Deming regression (intercept 0.65; slope 1.00) were not statistically significant (p > 0.05 for all). No significant difference was observed between the area under the ROC curves of CEA in the fresh and frozen specimens (p > 0.05 for all).ConclusionPleural fluid CEA is seemingly stable when stored at –80°C to −70°C for 1–3 years. Frozen storage does not significantly affect the diagnostic accuracy of CEA for MPE.
Increased heterozygosity in low‐pass sequencing data allows identification of blood chimeras in cattle
Authors: Lindtke Dorothea , Seefried Franz R. , Drögemüller Cord , Neuditschko Markus 
Published: June 2023

AbstractIn about 90% of multiple pregnancies in cattle, shared blood circulation between fetuses leads to genetic chimerism in peripheral blood and can reduce reproductive performance in heterosexual co‐twins. However, the early detection of heterosexual chimeras requires specialized tests. Here, we used low‐pass sequencing data with a median coverage of 0.64× generated from blood samples of 322 F1 crosses between beef and dairy cattle and identified 20 putative blood chimeras through increased levels of genome‐wide heterozygosity. In contrast, for 77 samples with routine SNP microarray data generated from hair bulbs of the same F1s, we found no evidence of chimerism, simultaneously observing high levels of genotype discordance with sequencing data. Fifteen out of 18 reported twins showed signs of blood chimerism, in line with previous reports, whereas the presence of five alleged singletons with strong signs of chimerism suggests that the in‐utero death rate of co‐twins is at the upper limit of former estimates. Together, our results show that low‐pass sequencing data allow reliable screening for blood chimeras. They further affirm that blood is not recommended as a source of DNA for the detection of germline variants.
Aspirations and investments in livestock: Evidence of aspiration failure in Kenya
Authors: Tabe‐Ojong Martin Paul Jr. , Heckelei Thomas , Rasch Sebastian 
Published: June 2023

AbstractAspirations influence future‐oriented behavior and ensuing outcomes but they may also fail to do so when the aspired‐to‐status is far away from the current one. Theoretical predictions suggest an inverted U‐shaped relationship between this aspiration gap and the effort to achieve what is aspired to. Aspirations that are ahead but not too far ahead of the current status serve as the best incentives for investments. We examine the income aspiration gap of smallholder households and relate it to livestock in a pastoral setting in Northern Kenya. Our focus on livestock is guided by the burgeoning recognition of livestock as an investment and saving conduit for many households in pastoral communities in developing nations. Employing different empirical strategies including parametric and semi‐parametric techniques, we find livestock to be increasing with aspirations up to a threshold, from which it then declines to lead to an aspiration failure. Delving into livestock heterogeneity, we uncover evidence that cattle and poultry respond more to the aspiration gap than small ruminants such as sheep and goats. Different U‐shaped tests confirm this relationship, bolstering the evidence of an aspiration failure. These findings are robust to the inclusion of relevant controls, truncations at zero, and different variable transformations. We also show that the findings are unlikely to be driven by unobserved heterogeneity. Additionally, we find that internal locus of control, that is the degree to which individuals believe they control outcomes in their lives is associated with livestock investments.
Less Volatile Value‐at‐Risk Estimation Under a Semi‐parametric Approach*
Authors: Huang Shih‐Feng , Wang David K. 
Published: June 2023

AbstractIn this study, we propose a two‐step, less‐volatile value‐at‐risk (LVaR) estimation using a generalized nearly isotonic regression (GNIR) model. In the proposed approach, a VaR sequence is first produced under the generalized autoregressive conditional heteroskedasticity (GARCH) framework. Then, the VaR sequence is adjusted by GNIR, and the generated estimate is denoted as LVaR. The results of an empirical investigation show that LVaR outperformed other VaR estimates under the classic equally weighted and exponentially weighted moving‐average frameworks. Furthermore, we show not only that LVaR is less volatile, but also that it performed reasonably well in various backtests.
Spatial transcriptomics combined with single‐cell RNA‐sequencing unravels the complex inflammatory cell network in atopic dermatitis
Authors: Mitamura Yasutaka , Reiger Matthias , Kim Juno , Xiao Yi , Zhakparov Damir , Tan Ge , Rückert Beate , Rinaldi Arturo O. , Baerenfaller Katja , Akdis Mübeccel , Brüggen Marie‐Charlotte , Nadeau Kari C. , Brunner Patrick M. , Roqueiro Damian , Traidl‐Hoffmann Claudia , Akdis Cezmi A. 
Published: June 2023

AbstractBackgroundAtopic dermatitis (AD) is the most common chronic inflammatory skin disease with complex pathogenesis for which the cellular and molecular crosstalk in AD skin has not been fully understood.MethodsSkin tissues examined for spatial gene expression were derived from the upper arm of 6 healthy control (HC) donors and 7 AD patients (lesion and nonlesion). We performed spatial transcriptomics sequencing to characterize the cellular infiltrate in lesional skin. For single‐cell analysis, we analyzed the single‐cell data from suction blister material from AD lesions and HC skin at the antecubital fossa skin (4 ADs and 5 HCs) and full‐thickness skin biopsies (4 ADs and 2 HCs). The multiple proximity extension assays were performed in the serum samples from 36 AD patients and 28 HCs.ResultsThe single‐cell analysis identified unique clusters of fibroblasts, dendritic cells, and macrophages in the lesional AD skin. Spatial transcriptomics analysis showed the upregulation of COL6A5, COL4A1, TNC, and CCL19 in COL18A1‐expressing fibroblasts in the leukocyte‐infiltrated areas in AD skin. CCR7‐expressing dendritic cells (DCs) showed a similar distribution in the lesions. Additionally, M2 macrophages expressed CCL13 and CCL18 in this area. Ligand–receptor interaction analysis of the spatial transcriptome identified neighboring infiltration and interaction between activated COL18A1‐expressing fibroblasts, CCL13‐ and CCL18‐expressing M2 macrophages, CCR7‐ and LAMP3‐expressing DCs, and T cells. As observed in skin lesions, serum levels of TNC and CCL18 were significantly elevated in AD, and correlated with clinical disease severity.ConclusionIn this study, we show the unknown cellular crosstalk in leukocyte‐infiltrated area in lesional skin. Our findings provide a comprehensive in‐depth knowledge of the nature of AD skin lesions to guide the development of better treatments.
Dilemmas of anthropological activism, solidarity, and human rights: Lessons from Haiti
Authors: Schuller Mark 
Published: June 2023

AbstractBuilding on a growing anthropological engagement with and interrogation of the multiple forms and meanings of activism, this article—based on over 20 years of activist engagement and ethnographic interviews spanning 11 years—offers ethnographically grounded understandings of solidarity activism. The rich and at times messy (auto)ethnographic data suggest that contradictions inherent to liberal humanism can increase hierarchies and social distance between groups across national boundaries. Further, new social media technologies notwithstanding, nongovernmental organizations (NGOs) remain hegemonic vehicles for this transnational exchange. The experience in Haiti, dubbed the “Republic of NGOs,” highlights contradictions within solidarity activism, generating a useful set of questions for other activist anthropologists and solidarity activists who work elsewhere. Moving beyond the discussion of what anthropology brings to activism, or the reverse, this article offers insights from ethnographic analyses of NGOs, or NGOgraphy, to critically understand and assess anthropological activism. Specifically, building off insights of “NGOing” as a verb, this article interrogates the (micro)politics, structures, and consequences of intervention. Further, international solidarity activism often operates on logics of projects and deliverables, and therefore NGOing can eclipse other “metrics,” disrupting and dividing local communities. Like NGOs, anthropologists function within a hierarchical transnational political economy and division of labor. [activist anthropology, Haiti, NGOs, solidarity, autoethnography]
Impact of cooperative membership on market performance of Nepali goat farmers
Authors: Neupane Huma , Paudel Krishna P. , He Qinying 
Published: June 2023

AbstractIn developing countries, agricultural cooperatives are increasingly used by farmers as a mechanism to gain market power in input and output markets. To assess the impact of cooperative membership on market channel selection and pricing outcomes, we conducted a survey of 661 Nepali goat farmers in 2019–20 and applied an endogenous switching probit model to analyze the data. Our findings indicate that cooperative membership had a significant and positive influence on farmers choosing cooperatives as their market channel. Additionally, farmers who sold their goats through cooperatives received significantly higher prices than those who sold through local markets or to goat collectors. We also observed that farmers who had access to price information were able to obtain better prices for their goats. Overall, our study highlights the potential benefits of promoting cooperative membership and marketing through cooperatives, as these efforts can help farmers improve the returns on their agricultural investments.
Faecal and urine metabolites, but not gut microbiota, may predict response to low FODMAP diet in irritable bowel syndrome
Authors: Wilson Bridgette , Kanno Tokuwa , Slater Rachael , Rossi Megan , Irving Peter M. , Lomer Miranda C. , Probert Chris , Mason A. James , Whelan Kevin 
Published: June 2023

SummaryBackgroundThe low FODMAP diet (LFD) leads to clinical response in 50%–80% of patients with irritable bowel syndrome (IBS). It is unclear why only some patients respond.AimsTo determine if differences in baseline faecal microbiota or faecal and urine metabolite profiles may separate clinical responders to the diet from non‐responders allowing predictive algorithms to be proposed.MethodsWe recruited adults fulfilling Rome III criteria for IBS to a blinded randomised controlled trial. Patients were randomised to sham diet with a placebo supplement (control) or LFD supplemented with either placebo (LFD) or 1.8 g/d B‐galactooligosaccharide (LFD/B‐GOS), for 4 weeks. Clinical response was defined as adequate symptom relief at 4 weeks after the intervention (global symptom question). Differences between responders and non‐responders in faecal microbiota (FISH, 16S rRNA sequencing) and faecal (gas–liquid chromatography, gas‐chromatography mass‐spectrometry) and urine (1H NMR) metabolites were analysed.ResultsAt 4 weeks, clinical response differed across the 3groups with adequate symptom relief of 30% (7/23) in controls, 50% (11/22) in the LFD group and 67% (16/24) in the LFD/B‐GOS group (p = 0.048). In the control and the LFD/B‐GOS groups, microbiota and metabolites did not separate responders from non‐responders. In the LFD group, higher baseline faecal propionate (sensitivity 91%, specificity 89%) and cyclohexanecarboxylic acid esters (sensitivity 80%, specificity 78%), and urine metabolite profile (Q2 0.296 vs. randomised −0.175) predicted clinical response.ConclusionsBaseline faecal and urine metabolites may predict response to the LFD.
Pola‐R‐CHP for frontline therapy in DLBCL: Are we saving money by spending more?
Authors: Vitolo U. , Frascione P. M. M. , Bonello F. 
Published: June 2023

The study by Kambhampati et al. offers the first European perspective on cost‐effectiveness of pola‐R‐CHP in the frontline line treatment of DLBCL patients. Nevertheless, the applicability of these results in other European settings remain questionable: Germany is indeed a wealthy country with wide access to cellular therapies in earlier lines, while this might not be the case for other European countries. The presented data must be re‐assessed when long term data on PFS and OS from the POLARIX trial are available, ideally considering also real‐life data. Similar CEAs in other European health care systems as well as in specific subgroups of patients are welcome to offer a broader perspective on the potential role of pola‐R‐CHP in Europe.Commentary on: Kambhampati et al. Cost effectiveness of polatuzumab vedotin in combination with chemoimmunotherapy (pola‐R‐CHP) in previously untreated diffuse large B‐cell lymphoma in Germany. Br J Haematol 2023;202:771–775.
Genes associated with spontaneous brain activity changes in clinically different patients with major depressive disorder: A transcription‐neuroimaging association study
Authors: Zhu Wenshuang , Liu Feng , Fu Jilian , Qin Wen , Xue Kaizhong , Tang Jie , Zhang Yong , Yu Chunshui 
Published: June 2023

AbstractAimsThe amplitude of low‐frequency fluctuations (ALFF) of resting‐state functional MRI signals is a reliable neuroimaging measure of spontaneous brain activity. Inconsistent ALFF alterations have been reported in major depressive disorder (MDD) possibly due to clinical heterogeneity. This study was designed to investigate clinically sensitive and insensitive genes associated with ALFF alterations in MDD and the potential mechanisms.MethodsTranscription‐neuroimaging association analyses of case–control ALFF differences from two independent neuroimaging datasets with gene expression data from Allen Human Brain Atlas were performed to identify the two gene sets. Various enrichment analyses were conducted to characterize their preference in biological functions, cell types, temporal stages, and shared effects with other psychiatric disorders.ResultsCompared with controls, first‐episode and drug‐naïve patients showed more extensive ALFF alterations than patients with varied clinical features. We identified 903 clinically sensitive genes and 633 clinically insensitive genes, and the former was enriched for genes with down‐regulated expression in the cerebral cortex of MDD patients. Despite shared functions of cell communication, signaling, and transport, clinically sensitive genes were enriched for cell differentiation and development whereas clinically insensitive genes were for ion transport and synaptic signaling. Clinically sensitive genes showed enrichment for microglia and macrophage from childhood to young adulthood in contrast to clinically insensitive genes for neurons before early infancy. Clinically sensitive genes (15.2%) were less likely correlated with ALFF alterations in schizophrenia than clinically insensitive genes (66.8%), and both were not relevant to bipolar disorder and adult attention deficit and hyperactivity disorder based on a third independent neuroimaging dataset.ConclusionsPresent results provide novel insights into the molecular mechanisms of spontaneous brain activity changes in clinically different patients with MDD.
Modeling population extirpation rates of white‐bellied and giant pangolins in Benin using validated local ecological knowledge
Authors: Zanvo Stanislas , Djagoun Chabi A. M. S. , Gaubert Philippe , Azihou Akomian F. , Jézéquel Céline , Djossa Bruno , Sinsin Brice , Hugueny Bernard 
Published: June 2023

AbstractPangolins are globally threatened by unsustainable hunting for local use and illegal international trade, plus habitat loss. In Benin (West Africa), white‐bellied and giant pangolins have experienced a contraction in their distribution areas and population decline during the last two decades. To better understand the factors underlying declines in these species, we investigated extirpation rates of populations over the last 20 years. Because pangolins are elusive species difficult to monitor by standard methods, the status of populations has been assessed through a local ecological knowledge (LEK) approach. We collected information on persistence or extirpation status of pangolins from 156 localities. A binomial model was built to predict population persistence probability as a function of past and ongoing landscape changes, initial abundance (1998), human pressures, and density of the protected area network. The LEK‐based model was highly accurate (97% correct classification rate) in predicting the presence of white‐bellied pangolin in 52 localities where its presence has been confirmed independently. According to model outputs, persistence probability of pangolins is positively related to distance to main road, initial population abundance, and negatively related to deforestation, shrinkage of favorable habitat, and distance to protected areas. When those factors are controlled for, the white‐bellied pangolin has a higher probability of persistence than the giant pangolin. Even assuming no further habitat change, the distribution area of the white‐bellied pangolin is predicted to keep decreasing against an unavoidable extinction of the giant pangolin in Benin in the next two decades. Besides validating the usefulness of LEK as a population assessment method, this study emphasizes that, despite a demonstrated positive effect of protected areas, the current situation is not sustainable for pangolins and calls for urgent conservation actions to stop or reduce overhunting.
A rare case of cutaneous pseudoglandular schwannoma
Authors: Doan Leandra , Cassarino David S. 
Published: June 2023

AbstractSchwannomas are benign tumors that arise from the peripheral nerve sheath. Many variants of schwannomas exist, including plexiform, epithelioid, cellular, glandular, and ancient. The pseudoglandular subtype is extremely rare, as fewer than five cases of cutaneous pseudoglandular schwannomas have been reported based on our literature review. Herein, we report a case of a 64‐year‐old female who presented with a skin‐colored nodule on her right arm for several years. Histopathology showed a superficial and deep dermal nodulocystic neoplasm composed of epithelioid and spindle cells surrounded by a fibrous stroma. The epithelioid cells surrounded multiple spaces suggestive of glandular differentiation, although many of these spaces also contained serum and red blood cells, raising consideration for vascular differentiation. Multiple epithelial markers, including pancytokeratin and epithelial membrane antigen, were all negative, providing no support for an epithelial tumor with true ductal/glandular differentiation. In addition, CD31, CD34, smooth muscle actin, and desmin stains were negative in these spaces, making a vascular neoplasm or smooth muscle tumor unlikely. However, SOX10 and S‐100 stains were positive, including in cells lining the pseudoglandular spaces, supporting the diagnosis of pseudoglandular schwannoma. Complete excision was recommended. This case highlights an extremely rare presentation of the pseudoglandular variant of schwannoma.
A case of reactive granulomatous dermatitis associated with neonatal lupus erythematosus
Authors: Xing Monica H. , Onajin Oluwakemi , Venkataraman Girish , Stein Sarah L. 
Published: June 2023

AbstractNeonatal lupus erythematosus (NLE) is an uncommon disorder affecting approximately one out of 20 000 live births in the United States. Common manifestations of NLE include cutaneous eruptions and cardiac involvement. The typical rash of NLE most closely resembles the rash of subacute cutaneous lupus erythematosus both clinically and histopathologically. We present a case of reactive granulomatous dermatitis (RGD) associated with NLE in a 3‐month‐old male in whom the initial histopathology and immunohistochemistry were concerning for hematologic malignancy. RGD is a unifying term used to describe cutaneous granulomatous eruptions that occur in response to a variety of stimuli, including autoimmune connective tissue diseases. Our case demonstrates the range of histopathological findings that may be present in the setting of NLE.