julilili42/papers huggingface dataset:
Peer Review Report For: Exploring the structural characteristics of the Adult Social Care Outcomes Toolkit (ASCOT) and ASCOT-Carer [version 2; peer review: 1 approved, 1 approved with reservations]
2023-03-27

Background : Measurement models inform the approach to assess a measure's validity and also how a measure is understood, applied and interpreted. With preference-based measures, it is generally accepted that they are formative ; however, if they are applied without preferences, they may be reflective , formative or mixed . In this study, we sought to empirically test whether the reflective , formative or mixed measurement model best describes PBMs of social care-related quality of life (ASCOT, ASCOT-Carer). We also explored the network approach, as an alternative. Methods : ASCOT and ASCOT-Carer data were analyzed using confirmatory factor analysis and Multiple Indicators Multiple Causes models to test reflective, formative or mixed measurement models, respectively. Network analysis of partial correlations using the Gaussian graphical model was also conducted. Results : The results indicated that the reflective measurement model is the worst fit for ASCOT and ASCOT-Carer. The formative or mixed models may apply to ASCOT. The mixed model was the best fit for ASCOT-Carer. The network analysis indicated that the most important or influential items were Occupation and Personal cleanliness and comfort (ASCOT) and Time and space and Self-care (ASCOT-Carer). Conclusions : The ASCOT and ASCOT-Carer are best described as formative/mixed or mixed models, respectively. These findings may guide the approach to the validation of cross-culturally adapted and translated versions. Specifically, we recommend that EFA be applied to establish structural characteristics, especially if the measure will be applied as a PBM and as a measure of SCRQoL. Network analysis may also provide further useful insights into structural characteristics.
Molecular Characterization of the ClpC AAA+ ATPase in the Biology of Chlamydia trachomatis
2023-03-28

Chlamydia trachomatis is an obligate intracellular pathogen and the world's leading cause of preventable infectious blindness and bacterial sexually transmitted infections. Due to the high prevalence of chlamydial infections along with negative effects of current broad-spectrum treatment strategies, new antichlamydial agents with novel targets are desperately needed.
Reversible Thermal Hysteresis in Heating‐Cooling Cycles of Magnetic Susceptibility: A Fine Particle Effect of Magnetite
2023-03-28

Abstract Thermomagnetic curves of magnetic susceptibility ( κ ) are key to characterizing magnetic properties. We report hump‐shaped κ ‐T curves of magnetite‐bearing basalt during heating‐cooling cycles to ∼340°C, with a large thermal hysteresis and similar starting and ending values, even in multiple repeated cycles, ruling out changes in magnetic mineralogy. Based on FORC diagrams and published results of engineered materials, we propose that thermal hysteresis arises from configurations of magnetic moments in clusters of single‐domain particles due to dipolar coupling, with different collective behavior during heating and cooling. This effect modifies the hump‐shaped thermal relaxation behavior of the individual nanoparticles. FORC and κ ‐T results indicate an increase in effective particle sizes after 700°C‐heating. Our results are a warning against premature interpretation of a decreasing trend in κ ‐T curves by maghemite inversion. Instead, fine particle behavior should be considered when a hump‐shaped κ ‐T behavior is detected.
Anoxygenic phototrophic arsenite oxidation by a Rhodobacter strain
2023-03-28

Abstract Microbially mediated arsenic redox transformations are key for arsenic speciation and mobility in rice paddies. Whereas anaerobic anoxygenic photosynthesis coupled to arsenite (As(III)) oxidation has been widely examined in arsenic‐replete ecosystems, it remains unknown whether this light‐dependent process exists in paddy soils. Here, we isolated a phototrophic purple bacteria, Rhodobacter strain CZR27, from an arsenic‐contaminated paddy soil and demonstrated its capacity to oxidize As(III) to arsenate (As(V)) using malate as a carbon source photosynthetically. Genome sequencing revealed an As(III)‐oxidizing gene cluster ( aioXSRBA ) encoding an As(III) oxidase. Functional analyses showed that As(III) oxidation under anoxic phototrophic conditions correlated with transcription of the large subunit of the As(III) oxidase aioA gene. Furthermore, the non‐As(III) oxidizer Rhodobacter capsulatus SB1003 heterologously expressing aioBA from strain CZR27 was able to oxidize As(III), indicating that aioBA was responsible for the observed As(III) oxidation in strain CZR27. Our study provides evidence for the presence of anaerobic photosynthesis‐coupled As(III) oxidation in paddy soils, highlighting the importance of light‐dependent, microbe‐mediated arsenic redox changes in paddy arsenic biogeochemistry.
Treatment and survival of patients with malignant ovarian sex cord‐stromal cell tumours: An analysis of the Arbeitsgemeinschaft für Gynäkologische Onkologie (AGO) study group CORSETT database
2023-03-28

Abstract Background Malignant sex cord‐stromal cell tumours (SCST) account for only 7% of ovarian malignancies. The Arbeitsgemeinschaft fuer Gynaekologische Onkologie (AGO) study group has established a clinicopathological database to provide an overview of the current treatment strategies and survival of SCST patients and to identify research needs. Methods Twenty centres provided mixed retro‐ and prospective data of patients with tumour specimens and second‐opinion pathology review treated between 2000 and 2014. Descriptive analyses of treatment strategies, Kaplan–Meier curves and cox regression analyses were conducted. Results Two hundred and sixty‐two SCST patients were included. One hundred and ninety‐one Granulosa‐cell tumour (GCT) and 17 Sertoli‐Leydig cell tumour (SLCT) patients were stage I disease (&gt;80%). Forty four GCT (18.7%) and two (8.3%) SLCT patients received adjuvant systemic treatment. After a median observation time of 78.2 months, 46% of all SCST patients experienced disease recurrence, treated predominantly with secondary debulking surgery (&gt; 90%). Advanced FIGO stage, lymph node involvement and intra‐operative capsule rupture were associated with disease recurrence on univariate analysis (all p &lt; 0.05). Median OS time was not reached. Discussion In this analysis of SCST patients, adjuvant chemotherapy was unable to prevent disease recurrence. Despite high recurrence rates, overall survival rates were excellent.
Tackling Misinformation with Games: A Systematic Literature Review
2023-03-28

Misinformation and fake news are severe threats to society. Despite the promising results of game-based interventions to mitigate the effects of misinformation, the corpus of research on critical reading games needs an overview. Therefore, a systematic literature review was conducted to analyze how games have been used to tackle misinformation and reveal trends in the design of critical reading games. A total of 15 papers eventually met the defined inclusion criteria and were analyzed. The review revealed that the use of games in critical reading education had emerged recently and focused mainly on fake news. Most games were grounded on inoculation theory and consequently designed to expose players to weakened doses of the misinformation manipulation techniques to build resistance against them. So far, the games have been studied mainly in informal settings and with adult participants. The median sample size was 196, and the median playing time was 15 minutes across the studies reported in the papers. Although all the reviewed papers reported positive outcomes, the game-based learning research on the critical reading domain is not yet mature enough to generalize findings.
The Great Ecological Transformation
2023-03-28

This article offers a theological rationale for engaging in a great ecological transformation. The author argues that this transformation cannot be achieved solely with technological means. Rather, we need far more than a great industrial transformation. We also need ecological justice that gives the nature of the earth and the animals their rights; recognition that ecological justice is related to social justice and, especially, to the rights of future generations; a new understanding of nature that liberates the nature of the earth from its modern, alienated status as a mere object; a new understanding of humanity that embeds human beings in the community of creation; and finally, a new cosmic spirituality that sanctifies lived life and engenders “respect for life” for everything that lives.
People with a tobacco use disorder misattribute non-drug cues as worse predictors of positive outcomes compared to drug cues
2023-03-28

Abstract Adaptive behaviours depend on dynamically updating internal representations of the world based on the ever-changing environmental contingencies. People with a substance use disorder (pSUD) show maladaptive behaviours with high persistence in drug-taking, despite severe negative consequences. We recently proposed a salience misattribution model for addiction (SMMA; Kalhan et al., (2021)), arguing that pSUD have aberrations in their updating processes where drug cues are misattributed as strong predictors of positive outcomes, but weaker predictors of negative outcomes. We also argue that conversely, non-drug cues are misattributed as weak predictors of positive outcomes, but stronger predictors of negative outcomes. However, these hypotheses need to be empirically tested. Here we used a multi-cue reversal learning task, with reversals in whether drug or non-drug cues are currently relevant in predicting the outcome (monetary win or loss). We show that compared to controls, people with a tobacco use disorder (pTUD), do form misaligned internal representations. We found that pTUD updated less towards learning the drug cue’s relevance in predicting a loss. Further, when neither drug nor non-drug cue predicted a win, pTUD updated more towards the drug cue being relevant predictors of that win. Our Bayesian belief updating model revealed that pTUD had a low estimated likelihood of non-drug cues being predictors of wins, compared to drug cues, which drove the misaligned updating. Overall, several hypotheses of the SMMA were supported, but not all. Our results implicate that strengthening the non-drug cue association with positive outcomes may help restore the misaligned internal representation in pTUD.
Funerary practices in megalithic tombs during the Argaric Bronze Age in South-Eastern Iberia: The cemetery of Los Eriales
2023-03-29

The transition between the Copper Age and the Argaric Bronze Age in south-eastern Iberia has traditionally been&#13;\\nunderstood in an evolutionary framework that would have involved the replacement of some cultural forms by&#13;\\nothers. The chronology of megalithic societies has changed this assumption, revealing that the continuity of&#13;\\nancestral funerary practices is also a key feature of the Bronze Age. In this context, the new radiocarbon series&#13;\\nfrom Los Eriales discussed in this paper can be considered a key contribution. Three main aspects stand out&#13;\\naccording to their statistical analysis: i) Los Eriales should be considered the most recent Iberian megalithic&#13;\\ncemetery, as ritual activity began in the last centuries of the third millennium cal BC; ii) funerary activity took&#13;\\nplace during short events of intensive ritual depositions spanning a few decades, mainly in the 21st and 18th&#13;\\ncenturies; and iii) Los Eriales cemetery was mainly used during the Argaric period, which means the coexistence&#13;\\nof two very different funerary practices: collective megalithic rituals and individual intramural inhumations. The&#13;\\ncontinuity of megalithic rituals can be explained in terms of resilience to the social fragmentation that characterised&#13;\\nArgaric societies.
Continuous cultivation of the lithoautotrophic nitrate‐reducing Fe( II )‐oxidizing culture KS in a chemostat bioreactor
2023-03-29

Abstract Laboratory‐based studies on microbial Fe(II) oxidation are commonly performed for 5–10 days in small volumes with high substrate concentrations, resulting in geochemical gradients and volumetric effects caused by sampling. We used a chemostat to enable uninterrupted supply of medium and investigated autotrophic nitrate‐reducing Fe(II)‐oxidizing culture KS for 24 days. We analysed Fe‐ and N‐speciation, cell‐mineral associations, and the identity of minerals. Results were compared to batch systems (50 and 700 mL—static/shaken). The Fe(II) oxidation rate was highest in the chemostat with 7.57 mM Fe(II) d −1 , while the extent of oxidation was similar to the other experimental setups (average oxidation of 92% of all Fe(II)). Short‐range ordered Fe(III) phases, presumably ferrihydrite, precipitated and later goethite was detected in the chemostat. The 1 mM solid phase Fe(II) remained in the chemostat, up to 15 μM of reactive nitrite was measured, and 42% of visualized cells were partially or completely mineral‐encrusted, likely caused by abiotic oxidation of Fe(II) by nitrite. Despite (partial) encrustation, cells were still viable. Our results show that even with similar oxidation rates as in batch cultures, cultivating Fe(II)‐oxidizing microorganisms under continuous conditions reveals the importance of reactive nitrogen intermediates on Fe(II) oxidation, mineral formation and cell–mineral interactions.
Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome
2023-03-29

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only <i>WNT4</i> (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce <i>GREB1L</i> findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with <i>GREB1L</i> variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel <i>GREB1L</i> variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in <i>GREB1L</i> (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. <i>GREB1L</i> variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of <i>GREB1L</i> to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.
Arabidopsis thalianaLSM7 is essential for auxin-mediated regulation ofSAURgenes and thermomorphogenesis
2023-03-29

Abstract Temperature affects plant growth by modulating the expression of genes and subsequent processing of RNAs that govern essential physiological processes. Here, we show that Arabidopsis thaliana Sm-like7 (LSM7), a core component of the splicing and decapping machinery, is indispensable for embryogenesis and development. Hypomorphic lsm7-2 mutants display severe developmental defects that are exacerbated by high temperatures. Transcriptome analysis verified LSM7’s extensive role in gene regulation. In particular, we found that the key regulator of thermomorphogenesis, PHYTOCHROME INTERACTING FACTOR 4 ( PIF4 ), and auxin-related genes, including SMALL AUXIN UP-REGULATED ( SAUR ) genes, are misregulated in lsm7-2 . Auxin metabolic profiling confirmed that auxin homeostasis was disturbed in lsm7-2 . Importantly, overexpression of the auxin-responsive SAUR19 gene partially restored thermomorphogenesis defects in lsm7-2 under high ambient temperature. Taken together, our research provides mechanistic insights into the interplay between RNA processing, hormone homeostasis, and the response to temperature regulation in plants and elucidates LSM7’s essential function in plant temperature acclimation and resilience. Significance Statement Given their sessile nature, plants cannot escape adverse environmental conditions such as cold or heat. Instead, they continuously adjust their gene expression and RNA processing to regulate growth and physiology in response to their surroundings. In this study, we investigated the role of the core RNA processing factor LSM7 in temperature acclimation in Arabidopsis thaliana . We found that LSM7 knockdown mutants were impaired in thermomorphogenesis and, as a result, were hypersensitive to elevated temperatures. At the molecular level, we demonstrated that this temperature sensitivity was caused by the misregulation of key regulators of thermomorphogenesis, including PIF4, auxin homeostasis and signaling, and SAUR genes. Our findings provide valuable insights into the role of RNA processing in plant temperature acclimation.
New evidence for Middle Bronze Age chronology from the Syro-Anatolian frontier
2023-03-29

Dates differ by up to 150 years in the protracted debate around the chronology of the Middle Bronze Age Near East. Here, the authors present radiocarbon and ceramic evidence from destroyed buildings at Zincirli, Türkiye, that support the Middle Chronology. Ceramics from late Middle Bronze Age sites in Syria and Anatolia, and Bayesian modelling of 18 well-stratified radiocarbon samples from site destruction contexts attributable to Hittite king Ḫattusili I, indicate a date in the later seventeenth century BC. Since the Northern Levant connects the Mesopotamian and Eastern Mediterranean second-millennium BC chronologies, this evidence supports the convergence of these long-debated schemas, with implications for the start of the Late Bronze Age and the rise of empires.
The photoreceptor protective cGMP‐analog Rp‐8‐Br‐PET‐cGMPS interacts with cGMP‐interactors PKGI, PDE1, PDE6, and PKAI in the degenerating mouse retina
2023-03-29

Abstract The inherited eye disease retinitis pigmentosa (RP) causes the loss of photoreceptors by a still unknown cell death mechanism. During this degeneration, cyclic guanosine‐3′,5′‐monophosphate (cGMP) levels become elevated, leading to over‐activation of the cGMP‐binding protein cGMP‐dependent protein kinase (PKG). cGMP analogs selectively modified to have inhibitory actions on PKG have aided in impeding photoreceptor death, and one such cGMP analog is Rp‐8‐Br‐PET‐cGMPS. However, cGMP analogs have previously been shown to interact with numerous targets, so to better understand the therapeutic action of Rp‐8‐Br‐PET‐cGMPS, it is necessary to elucidate its target‐selectivity and hence what potential cellular mechanism(s) it may affect within the photoreceptors. Here, we, therefore, applied affinity chromatography together with mass spectrometry to isolate and identify Rp‐8‐Br‐PET‐cGMPS interactors from retinas derived from three different murine RP models (i.e., rd1, rd2 , and rd10 mice). Our findings revealed that Rp‐8‐Br‐PET‐cGMPS bound seven known cGMP‐binding proteins, including PKG1β, PDE1β, PDE1c, PDE6α, and PKA1α. Furthermore, an additional 28 proteins were found to be associated with Rp‐8‐Br‐PET‐cGMPS. This latter group included MAPK1/3, which is known to connect with cGMP/PKG in other systems. However, in organotypic retinal cultures, Rp‐8‐Br‐PET‐cGMPS had no effect on photoreceptor MAPK1/3 expression or activity. To summarize, Rp‐8‐Br‐PET‐cGMPS is more target specific compared to regular cGMP.
Addressing fragmented human–nonhuman interactions through anubuntu‘mixed’ ethics
2023-03-29

Abstract In this paper, I address human‐induced environmental ills we face using an ubuntu‐ inspired ethical lens. I follow ubuntu scholars to stress the significance for moral agents to embody virtues. Virtue development is essential to carry out obligations and address human impacts on the environment. Thaddeus Metz, in particular, has drawn attention to how embodying ubuntu virtues of humility and friendliness can prompt moral agents to be other‐regarding. The view I developed in this paper differs from his ubuntu ‐inspired account in at least two significant ways. First, humans cannot be in harmonious relationships with some species such as Black Mambas, Hyenas and sea urchins even if they can interact. Second, we must acknowledge the consequentialist dimension of ubuntu ethics and prioritise the different aspects of ubuntu ‘mixed’ ethics, ranking them to offer possibilities for a more realistic recommendation to change our moral life. This paper demonstrates that the three dimensions of ubuntu ‘mixed’ ethics are fundamental because we need to think about moral consequences, right action and our virtue in accounting for our actions.
Clinically meaningful metrics of speech in neurodegenerative disease: Quantification of speech intelligibility and naturalness in ataxia
2023-03-29

Abstract Background Digital biomarkers continue to make headway in the clinic and clinical trials for neurological conditions. Speech is a domain with great promise. Objectives Using Friedreich ataxia (FRDA) as an exemplar population, we aimed to align objective measures of speech with markers of disease severity, speech related quality of life and subjective judgements of speech using supervised machine learning techniques. Methods 132 participants with genetically confirmed diagnosis of FRDA were assessed using digital speech tests, disease severity scores (Friedreich Ataxia Rating Scale, FARS) and speech related quality of life ratings over a 10-year period. Speech was analyzed perceptually by expert listeners for intelligibility (ability to be understood) and naturalness (deviance from healthy norm) and acoustically across 344 features. Features were selected and presented into a random forest and a support vector machine classifier in a standard supervised learning setup designed to replicate expert-produced scores. Results We demonstrate a subset of measures are strongly associated with all four clinical scales. Objective speech data replicated experts’ assessments of naturalness and intelligibility. These scores represent a lower level of variability than observed between subjective listener ratings. Findings provide evidence there are specific objective markers of speech that change over time and reflect clinical aspects of the disease. Discussion The use of a large dataset yielded a speech assay capable of accurately approximating expert listener ratings of key clinical aspects of dysarthria severity. Distinct but complementary subsets align with disease severity and speech related quality of life.