julilili42/papers huggingface dataset:
Shipment of Cyanobacteria by Agarose Gel Embedding (SCAGE)&mdash;A Novel Method for Simple and Robust Delivery of Cyanobacteria
2024-01-01

In modern science, the exchange of scientific material between different institutions and collaborating working groups constitutes an indispensable endeavor. For this purpose, bacterial strains are frequently shipped to collaborators to advance joint research projects. Bacterial strains are usually safely shipped as cultures on solid medium, whereas the shipment of liquid cultures requires specific safety measures due to the risk of leakage. Cyanobacterial cultures are frequently maintained as liquid stock cultures, and this problem typically arises. This protocol describes a new method for the shipment of liquid cyanobacterial stock cultures by agarose gel embedding (SCAGE). More specifically, a cyanobacterial culture is mixed with low-melting agarose and cast into sterile plastic bags, resulting in a thin, solid cyanobacterial agarose gel (cyanogel) that can be easily shipped. After delivery, subsequent regeneration of the cyanogel material in liquid media results in full recovery of the examined bacterial strains. Thus, the packaging method devised in the present study comprises an innovative technique to facilitate the shipment of bacterial strains, whilst eliminating previously encountered issues like cell culture leakage. Key features • New packaging procedure to reduce culture leakage. • Novel technique facilitating improved shipment conditions. • Validated method leading to recovery of tested bacterial strains after 14 days. Graphical overview Schematic representation of steps for gel embedding and recovery of cyanobacteria.
Spatial effects with missing data
2024-01-01

Abstract In recent years, there has been an increased attention and interest in quantitative and statistical models of language contact and language diffusion in space. This article presents an improved model, multivAreate 2, to estimate spatial and contact relations between languages and dialects based on work by Guzmán Naranjo and Mertner ((2022). Estimating areal effects in typology: A case study of african phoneme inventories. Journal of Linguistic Typology 27(2), 455–80) and Ranacher et al. ((2021). Contact-tracing in cultural evolution: A Bayesian mixture model to detect geographic areas of language contact. Journal of the Royal Society Interface 18(181), 1–15). We test our model on three different datasets: Balkans, South America (Ranacher et al. (2021). Contact-tracing in cultural evolution: A Bayesian mixture model to detect geographic areas of language contact. Journal of the Royal Society Interface 18(181), 1–15), and the Americas (Urban et al., (2019). The areal typology of western middle and south america: Towards a comprehensive view. Linguistics 57(6), 1403–63). We show that this new model can address shortcomings found in previous models, and it offers some useful tools for researchers working on contact and areal linguistics.
The ambiguous other. Engaging with far right and other uncomfortable subjectivities
2024-01-01

Abstract: This article explores anthropological hesitation in engaging with “abject” or otherwise “uncomfortable” subjectivities, identifying some of the main concerns and challenges behind it. In doing so, the discussion focuses on far-right subjectivities and on the reasons behind the relative lack of ethnographic studies thereof. Among other things, it is argued that the far-right other does not fit current anthropological orthodoxy in terms of ethnographic approach and therefore represents a kind of ambiguous alterity that poses ethical and methodological challenges for anthropologists. The discussion then brings to light some of the tensions and dilemmas inherent in anthropological approaches to uncomfortable alterities. The article concludes by highlighting what may be at stake for anthropology when excluding certain subjects of research, suggesting instead that their study offers opportunities to expand anthropological horizons of knowledge production, increasing the discipline’s relevance for understanding and analysing complex and troubling contemporary social phenomena.
P905 Symptomatic remission and IUS improvements in a multi-national real-world cohort of UC patients treated with Upadacitinib - First results from the IBD-DACH study EUROPE
2024-01-01

Abstract Background Upadacitinib (UPA) is an oral, reversible and selective Januskinase-inhibitor (JAKi) that was approved for the treatment of several immune-mediated inflammatory diseases, including moderate to severe ulcerative colitis (UC) (1). While the efficacy of UPA has been demonstrated in clinical trials in UC, real-word (RW) evidence on the effectiveness and safety of UPA in UC remains scarce (2). Here, we shed light on the clinical and sonographic results after 2 and 8 weeks of UPA induction in a large, multinational RW cohort of UC patients. Methods EUROPE is an ongoing, prospective, non-interventional, multi-country study in patients with active UC who initiate therapy with UPA. The study assesses the early clinical effectiveness and the predictive value of early disease improvements including sonographic parameters for the long-term outcome after 52 and 104 weeks. For this interim analysis, we report clinical and sonographic results at baseline (BL), week 2 (2W) and week 8 (8W) of 124 UC patients with a visit after 8W until August 2023. For 75 patients, sonographic BL data for the most affected bowel segment was available. Results Of the 124 UC patients, most were male (60.5%, n = 75) with a median age and disease duration of 37.5 years (27.5 – 50.9) and 6.58 years (2.40–12.13). Almost half of all patients had a pancolitis (48.4%, n = 60) The vast majority of patients was bio-experienced (85.5%, n = 106), a third had been exposed to ≥ 3 biologicals (28.2%, n = 35). At BL, patients had a median bowel wall thickness (BWT) of 5.0 mm (3.8-7.0) in the sigmoid colon. It was the most affected segment in 44.4% of patients (n = 55). Disease activity per paMayo score was 3.0 (2.0-5.0) points, with 72.6% (n = 90) and 38.8% (n = 48) of patients reporting ≥ 3 more stools than usual/day and blood in most stools or bleeding without stool, respectively. At 2W after UPA induction, stool frequency and rectal bleeding substantially improved as reflected by the rate of patients in symptomatic remission significantly increasing from 16.9% (n = 21) at BL to 43.5% (n = 54) at 2W and to 64.5% (n = 80) at W8 (both p &amp;lt; 0.001 vs. BL, fig.1). BWT was reduced significantly as early as 2W (n = 48; p &amp;lt; 0.001) and was ≤ 3mm in more than half of all patients. Considering the overall population, 156 patients were included in the safety analysis. Of these, 23.7% (n = 37) experienced an adverse event of which most were non-serious. Conclusion In this first interim analysis of the EUROPE study, UPA treatment in UC was associated with early clinical and sonographic improvement, with most patients achieving symptomatic remission and/or normalization of BWT by week 8 of treatment. 1-SmPC Upadacitinib 2-Danese, Vermeire et al. Lancet. 2022 Jun 4;399(10341):2113-2128
A zooarchaeological perspective on late pleistocene/early holocene human behaviour in the Maloti-Drakensberg region, southern Africa: The view from Ha Makotoko and Ntloana Tšoana rock-shelters, Lesotho
2024-01-01

Re-excavation of Ha Makotoko and Ntloana Tšoana rock-shelters in western Lesotho, produced abundant faunal remains (both macro and micro) from people using the Robberg technocomplex during the late Pleistocene (Ha Makotoko and Ntloana Tšoana (15.4–13.4 kcal. BP) and early Holocene (Ntloana Tšoana 11.1–10.2 kcal. BP). This faunal material allows us to identify the subsistence strategies they employed, using the unbiased Simpson's evenness index (1-D′), and Shannon's evenness index to track diet breadth. Detailed analyses of the sites' microfauna indicates that eagle owls and/or small carnivores — not humans — were responsible for introducing them into the deposits. A chi-squared test comparing diet breadth across the sites identifies hunting strategy, focused on size 2 and 3 migratory ungulates (equids, suids, and bovids), supplemented with size 1 and 4 bovids. Comparing the evenness values from Ha Makotoko and Ntloana Tšoana to published data from other Robberg-associated sites in the wider Maloti-Drakensberg region (Sehonghong, Rose Cottage Cave and Tloutle) allows variability in subsistence strategies to be addressed. A chi-squared test comparing ungulate size classes, small mammals and fish with the evenness index reveals two important statistical differences: the warm period occupation (16.5–14.3 kcal. BP) at Rose Cottage Cave presents a narrow diet heavily focused on size 3 ungulates (with a lack of fish). At the other end of the climate spectrum, cold conditions at Sehonghong immediately before the Last Glacial Maximum were associated with a narrow diet focused on intensive fishing, with lower-than-expected numbers of size 3 ungulates. The deposits at Ntloana Tšoana, Ha Makotoko, and Tloutle, along with the Younger Dryas-associated assemblage from Sehonghong, on the other hand, present broad diets. Fish and small mammals make more of a contribution to the expanding diet in the highlands. Our approach demonstrates the flexibility that makers of Robberg tools displayed in adapting to the changing climatic and ecological conditions of this high-elevation region in the interior of southern Africa during Marine Isotope Stage 2 and across the Pleistocene/Holocene transition.
Eight Rules for Implication Elimination
2024-01-01

Eight distinct rules for implication in the antecedent for the sequent calculus, one of which being Gentzen's standard rule, can be derived by successively applying a number of cuts to the logical ground sequent A → B, A ⇒ B. A naive translation into natural deduction collapses four of those rules onto the standard implication elimination rule, and the remaining four rules onto the general elimination rule. This collapse is due to the fact that the difference between a formula occurring in the succedent of a premise of a sequent calculus rule and that formula instead occurring in the antecedent of the conclusion cannot be adequately expressed in the framework of natural deduction. In contrast to this, the difference between a formula occurring in the succedent of the conclusion of a sequent calculus rule and that formula instead occurring in the antecedent of a premise corresponds exactly to the distinction between the standard implication elimination rule and its general counterpart. This incongruity can be remedied by introducing a notational facility that requires of the particular premise of a rule to which it is attached to be an assumption, i.e., to prevent it from being the conclusion of another rule application. Applying this facility to implication elimination results in eight distinct rules that correspond exactly to the eight sequent calculus rules. These eight rules are presented and discussed in detail. It turns out that a natural deduction calculus (for positive implication logic) that employs the rule corresponding to the standard left implication rule of the sequent calculus as well as a rule for explicit substitution can be seen as a natural deduction style sequent calculus.
Embracing digital health: German otolaryngology patients’ usage and prospects of digital information and communication technologies for cross-sectoral care
2024-01-01

Objective The usage of digital information and communication technologies in European healthcare is growing. Unlike numerous technological possibilities, the present use of these technologies and perspectives towards them in relation to otolaryngology care have so far been of less interest. This study evaluates the utilisation of and attitudes towards digital information and communication technologies in cross-sectoral otolaryngology care among German patients. Methods A structured interview-based study was conducted at the outpatient facility of a tertiary hospital in Germany. It focused on chief complaints, current use of digital technologies, estimated benefits of increased digital technology use in otolaryngology care, and sociodemographic data. The detailed statistical analysis employed Chi-squared tests and multivariate logistic regression. Results A total of 208 otolaryngology patients completed the interview. Digital communication technologies exhibited a high penetration rate (91.8%) and were regularly used in daily life (78.7%) and for health reasons (73.3%). Younger age ( p ≤ 0.003) and higher education levels ( p ≤ 0.008) were significantly correlated with the increased digital communication technology use. The overall potential of eHealth technologies was rated significantly higher by younger patients ( p ≤ 0.001). The patients’ chief complaints showed no significant influence on the current and potential use of these technologies for cross-sectoral otolaryngology care. Conclusion Regardless of their chief complaints, German otolaryngology patients regularly use digital information and communication technologies for health reasons and express interest in their further use for cross-sectoral care. To enhance digital patient communication in otolaryngology, attention should be given to treatment quality, usability, data security and availability and financial remuneration for service providers.
Melanoma-specific survival of patients with uveal melanoma and liver metastases diagnosed between 2005 and 2021
2024-01-01

Background: Uveal melanoma is the most common malignant tumor of the eye in adults. About half of the patients develop distant metastases, most commonly liver metastases (&gt;90%). These are associated with poorer overall survival compared to patients with extrahepatic metastases. Patients and methods: In this retrospective study, patients diagnosed with metastatic uveal melanoma between January 2005 and December 2021 and treated at the Center for Dermato-oncology at the University of Tübingen, were included. The total cohort was divided into two groups. Group 1, in which the first diagnosis of metastasis was between 2005 and 2015 and group 2 with first metastasis between 2016 and 2021. Melanoma-specific survival (MSS) and progression-free survival (PFS) were calculated with the Kaplan-Meier method, test for differences was performed by the log-rank test. Results: A total of 167 patients were included in the study. Since more than 90% of patients had developed liver metastases as their first site of metastasis, we focused our analysis on patients with liver metastases. Median MSS was 28 months (95% confidence interval (CI) (22.8–33.2 months)) in patients receiving first-line liver-directed therapy ( n = 89) compared to 10 months (95% CI (8.4–11.6 months)) for patients with first-line systemic therapy ( n = 45). The best MSS was found in patients of group 2 and liver-directed therapy as first-line treatment. Since survival with first-line liver-directed therapy was significantly better in group 2, subsequent systemic therapies must also be considered, especially immune checkpoint inhibitors. Conclusion: This analysis revealed that MSS has improved significantly in recent years. In our analysis, first-line liver-directed therapy was associated with improved survival compared to first-line systemic therapy. Further studies are urgently needed, for example, to investigate the combination of immune checkpoint inhibition or tebentafusp with liver-specific procedures from the outset.
Group Coordination Catalyzes Individual and Cultural Intelligence
2024-01-01

Abstract A large program of research has aimed to ground large-scale cultural phenomena in processes taking place within individual minds. For example, investigating whether individual agents equipped with the right social learning strategies can enable cumulative cultural evolution given long enough time horizons. However, this approach often omits the critical group-level processes that mediate between individual agents and multi-generational societies. Here, we argue that interacting groups are a necessary and explanatory level of analysis, linking individual and collective intelligence through two characteristic feedback loops. In the first loop, more sophisticated individual-level social learning mechanisms based on Theory of Mind facilitate group-level complementarity, allowing distributed knowledge to be compositionally recombined in groups; these group-level innovations, in turn, ease the cognitive load on individuals. In the second loop, societal-level processes of cumulative culture provide groups with new cognitive technologies, including shared language and conceptual abstractions, which set in motion new group-level processes to further coordinate, recombine, and innovate. Taken together, these cycles establish group-level interaction as a dual engine of intelligence, catalyzing both individual cognition and cumulative culture.
A Rhetoric of Cooperation: How Swedish parties argued in parliament 2015 and 2016 after the migration agreement
2024-01-01

The aim of this topos analysis is to identify features of argumentation in Swedish parliamentary debates on asylum policy in 2015 and 2016 compared to German debates. Findings include a focus on procedural rather than substantive aspects and an adaptation of government-like argumentation by cooperating opposition parties. These can be attributed to the focus on consensus and cooperation in Sweden, governed by a minority government, and may be typical of minority governments, common in Scandinavia, in general.
Porcine ex vivo retina model to study retinal neurodegenerative diseases: Potential role of mesenchymal stem cells
2024-01-01

Aims/Purpose: Retinal neurodegenerative diseases (RND) are associated with a progressive degeneration and death of retinal cells. Recently, mesenchymal stem cells (MSCs) showed a protective role against retinal cells degeneration and apoptosis. However, due to the complexity of such diseases, there is the need to develop in vitro or ex vivo models which allow the study of RND pathogenesis and better understand the regenerative role of MSCs. Therefore, the aim of our study was to use porcine retinas to establish a possible ex vivo model of spontaneous neuroretinal degeneration and employ this model to evaluate the efficacy of human amniotic fluid stem cells (hAFSCs) on retinal cells undergoing damage. Methods: To this end, neuroretinal explants were obtained from pig eyes and placed over the porous membrane of a transwell plate. To induce a time‐dependent spontaneous retinal degeneration, explants were cultured for 24, 48, 72, 96 h, 5 and 8 days. The damage grade was assessed with qRT‐PCR and immunohistochemistry analyses for GFAP and TUNEL‐assay. Then, the explants were co‐cultured with hAFSCs up to 8 days to evaluate their effect on retinal cells death via propidium iodide (PI) staining. Results: Results demonstrated that the cultivation of retinal explants up to 8 days induced an increase in the gene expression of inflammatory (NF‐kB and TNF‐alpha), pro‐apoptotic (p21 and p53) and oxidative stress markers (NRF2). We also observed an increased expression of GFAP and CD11b, suggesting an activation of the microglia and up‐regulation of Müller cells. In addition, the cultivation time induced an increase in the number of apoptotic cells (TUNEL). However, interestingly, the cells death decreased after co‐cultivation with hAFSCs (PI staining). Conclusions: In conclusion, our data demonstrate that the prolonged cultivation of porcine ex vivo retina can induce a time‐dependent spontaneous degeneration able to simulate a model of RND. Of note, the co‐culture preliminary data suggest a protective effects of hAFSCs on retinal cells death.
Decellularized human corneal lenticule as a delivery system of recombinant human nerve growth factor and human amniotic fluid stem cells factors for posterior ocular disease treatment
2024-01-01

Aims/Purpose: Posterior ocular diseases, such as glaucoma and diabetic retinopathy (DR), are the main causes of blindness worldwide. Among the possible therapeutic approaches particular interest was turned to neurotrophic factors, such as Nerve Growth Factor (NGF), and to mesenchymal stem cells (MSCs)‐derived factors. Nevertheless, the local drugs and factors delivery in the eye remains a challenge. Therefore, using an in vitro model of glaucoma and an ex vivo model of DR, this study aimed to test the feasibility to use decellularized human corneal lenticule (hCL) as natural delivery system able to vehicle neurotrophic and MSCs‐regenerative factors. Methods: hCLs (thickness 100–120 μm) collected from donors undergoing refractive surgery, were decellularized (0.1% SDS) and engineered with MSCs from human amniotic fluid (hAFSCs) and/or with microparticles containing rhNGF (rhNGF‐MPs). Human Trabecular Meshwork cells (HTMCs), damaged with Transforming Growth Factor‐β2 (TGF‐β2; 5 ng/mL for 4 days), were employed to mimic glaucoma condition in vitro. DR disease was reproduced using an ex vivo model of porcine retinal explants exposed to high glucose (HG; 25 mM for 4 days). Results: Results deriving from glaucoma model showed that the deposition of extracellular matrix and the specific protein expression of COL4a1, COL1a1 and ACTA1 were reduced following the HTMCs incubation with hCL engineered with hAFSCs or rhNGF‐MPs. Likewise, in the DR model, the HG‐increased Tumour Necrosis Factor α (TNF‐α) and Nuclear factor erythroid 2–Related Factor 2 (NRF2) levels were reduced following the incubation with hCL engineered with hAFSCs and rhNGF‐MPs. Of note, as demonstrated by the increase of structural (TUBB3 and Rho) and apoptotic (BAX/Bcl2 and p21) markers, a neuroprotective effect of engineered‐hCLs was observed in the DR model. Conclusions: Overall, our results demonstrated that this innovative bio‐engineered scaffold may represent a potential therapeutic approach for posterior ocular diseases treatment.
Mobile CRISPRi moves through the complexity of bacterial genetics
2024-01-01

In this issue of Cell Reports Methods, Rachwalski et al. describe a high-throughput method to screen genetic interactions in bacteria using a conjugative CRISPR interference (CRISPRi) plasmid. The method enables systematic studies of gene essentiality in diverse genomic and environmental contexts and is applicable to Escherichia coli as well as other bacteria.