Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Molecular Phylogeny of Salps (Tunicata: Thalicea: Salpida) and the Evolutionary History of Their Colonial Architecture

Synopsis Salps are marine pelagic tunicates with a complex life cycle, including a solitary and colonial stage composed of asexually budded individuals. These colonies develop into species-specific architectures with distinct zooid orientations, including transversal, oblique, linear, helical, and bipinnate chains, as well as whorls and clusters. The evolutionary history of salp colony architecture has remained obscured due to the lack of an ontology to characterize architectures, as well as a lack of phylogenetic taxon sampling and resolution of critical nodes. We (1) collected and sequenced eight species of salps that had never been sequenced before, (2) inferred the phylogenetic relationships among salps, and (3) reconstructed the evolutionary history of salp colony architecture. We collected salp specimens via offshore SCUBA diving, dissected tissue samples, extracted their DNA, amplified their 18S gene, and sequenced them using Sanger technology. We inferred the phylogeny of Salpida based on 18S using both Maximum Likelihood and Bayesian approaches. Using this phylogeny, we reconstructed the ancestral states of colony architecture using a Bayesian ordered Markov model informed by the presence and absence of specific developmental mechanisms that lead to each architecture. We find that the ancestral salp architecture is either oblique or linear, with every other state being derived. Moreover, linear chains have evolved independently at least three times. While transversal chains are developmentally basal and hypothesized to be ancestral, our phylogenetic topology and reconstructions strongly indicate that they are evolutionarily derived through the loss of zooid torsion. These traits are likely critical to multijet locomotory performance and evolving under natural selection. Our work showcases the need to study the broader diversity of salp species to gain a comprehensive understanding of their organismal biology, evolutionary history, and ecological roles in pelagic ecosystems.
Trajectory of Systemic Blood Pressure in Early Life: A Cohort Study

Objective. To track the BP (blood pressure) trajectory of healthy infants during the first year of life of healthy infants born in Northeast Brazil. Methods. In this cohort study, BP was assessed by oscillometry at the first 24 hours of life and 12 months of age. Results. Systolic blood pressure (SBP) and diastolic blood pressure (DBP) increased with age (P < .001) and were not influenced by gender (SBP: P = .178 and DBP: P = .623) or type of delivery (SBP: P = .827 and DBP: P = .106), when compared between the first 24 hours of life and 12 months of age. Conclusion. The data from the present study increased knowledge about the trajectory of BP during the first year of life. The increase in BP between the first month and the first year of life was not influenced by gender or type of delivery.
River Po discharges and cycles of solar activity

DISCUSSION Natural climatic changes and solar cycles: an analysis of hydrological time series' There is a tradition that the Editor invites discussion of every paper published in Hydrological Sciences Journal. In principle, the discussion period starts from the moment of publication of the paper in question and ends six months afterwards. Some time later, the discussion (or discussions) and authors' reply are published in one issue of the journal. In this issue, the original paper, the discussion and the reply are published next to each other. How did it happen? The authors of the original paper, accepted for publication in Hydrological Sciences Journal, sent their contribution to Dr Theodor Landscheidt, an expert in cycles of solar activity. Dr Landscheidt decided to make an interdisciplinary contribution in the form of a discussion. Under such circumstances, and for the benefit and convenience of our readership, the Editor has decided that all three items should be published in the same, present issue. The discussion foresees changes of solar parameters which may influence the process of river flow. It will be interesting to see how these forecasts fare in comparison to the data which will be observed in the near future. Do we witness the advent of an operational tool for medium-and long-term flow forecasting? Chaos theory teaches us that boundaries between different fields are rife with creative potential. The interdisciplinary paper "Natural climatic changes and solar cycles: an analysis of hydrological time series" by Tomasino & Dalla Valle (2000) is a case in point. It presents evidence that climate patterns in quite different world regions show common traits that point to forcing external to the Earth's climate system. The authors' frequency analysis shows that the most plausible external forcing agent, the Sun's varying activity, is involved in the common features. The spectrum of variations in the level of Lake Victoria yields a peak at 11 years, the well known period of the sunspot cycle. Yet the strongest peak in the analysis of River Po discharges appears at 8.7 years, a wavelength that most astrophysicists and climatologists do not associate with solar activity. So an explanation is in order, especially as the time series of River Po discharges is used by the authors to forecast periods of droughts and floods as well as instances of slime bloom in the Adriatic Sea.
Derivation of indirect predictions using genomic recursions across generations in a broiler population

Abstract Genomic estimated breeding values (GEBV) of animals without phenotypes can be indirectly predicted using recursions on GEBV of a subset. To maximize predictive ability of indirect predictions (IP), the subset must represent the independent chromosome segments segregating in the population. We aimed to 1) determine the number of animals needed in recursions to maximize predictive ability, 2) evaluate equivalency IP—GEBV, and 3) investigate trends in predictive ability of IP derived from recent vs. distant generations or accumulating phenotypes from recent to past generations. Data comprised pedigree of 825K birds hatched over 12 overlapping generations, phenotypes for body weight (BW; 820K), residual feed intake (RF; 200K) and weight gain during a trial period (WG; 200K), and breast meat percent (BP; 43K). A total of 154K birds (last six generations) had genotypes. The number of animals that maximize predictive ability was assessed based on the number of largest eigenvalues explaining 99% of variation in the genomic relationship matrix (1Me = 7,131), twice (2Me), or a fraction of this number (i.e., 0.75, 0.50, or 0.25Me). Equivalency between IP and GEBV was measured by correlating these two sets of predictions. GEBV were obtained as if generation 12 (validation animals) was part of the evaluation. IP were derived from GEBV of animals from generations 8 to 11 or generations 11, 10, 9, or 8. IP predictive ability was defined as the correlation between IP and adjusted phenotypes. The IP predictive ability increased from 0.25Me to 1Me (11%, on average); the change from 1Me to 2Me was negligible (0.6%). The correlation IP—GEBV was the same when IP were derived from a subset of 1Me animals chosen randomly across generations (8 to 11) or from generation 11 (0.98 for BW, 0.99 for RF, WG, and BP). A marginal decline in the correlation was observed when IP were based on GEBV of animals from generation 8 (0.95 for BW, 0.98 for RF, WG, and BP). Predictive ability had a similar trend; from generation 11 to 8, it changed from 0.32 to 0.31 for BW, from 0.39 to 0.38 for BP, and was constant at 0.33(0.22) for RF(WG). Predictive ability had a slight to moderate increase accumulating up to four generations of phenotypes. 1Me animals provide accurate IP, equivalent to GEBV. A minimum decay in predictive ability is observed when IP are derived from GEBV of animals from four generations back, possibly because of strong selection or the model not being completely additive.
Participant experiences in HIV cure-directed trial with an extended analytical treatment interruption in Philadelphia, United States

Background A feature of HIV cure trials is the need to interrupt treatment to test the efficacy of experimental interventions—a process known as analytical treatment interruptions (ATIs). Objectives We report the experiences of participants after they completed an extended ATI. Methods From April to November 2022, we conducted post-ATI in-depth interviews with BEAT2 clinical trial (NCT03588715) participants who stopped ART while receiving an immunotherapy regimen. We used conventional content analysis to code the data. Results We conducted interviews with 11 Black/African American and three White/Caucasian participants (11 males, two females, and one transgender woman). The mean ATI was 38 weeks. Participants noted several significant experiences surrounding the interventions’ side effects, ATI, and returning to medication. Some participants had positive experiences with their ATI. Other participants were nervous during the ATI. Rising viral loads led some to feel a sense of failure. Although trial experiences were heterogeneous, participants unanimously had positive interactions with the clinical trial staff which facilitated their retention in the trial. Participants shared their experiences with the trial, including changes in expectations, experiences with experimental interventions and procedures, compensation as a measure of respect, effort, transportation, and effects of COVID-19 during the trial. Based on these results, we provide considerations for the conduct of future HIV cure-directed clinical trials involving ATIs. Conclusions Managing expectations, focusing on participants’ contributions, and providing support to reduce feelings of having failed the research team and/or the HIV community following viral rebound should be part of HIV cure trial design. Discussing the mental health impact of rebound during consent, distinct from risk, is needed. Continued efforts to understand how people with HIV experience ATIs will improve future designs of HIV cure clinical trials.
Rheumatic masqueraders: mimics of primary vasculitis - a case-based review

ABSTRACT Introduction Vasculitis conditions are often serious and sometimes fatal diseases, therefore it is paramount to diagnose correctly and treat appropriately. Mimics of primary vasculitis can include either non-inflammatory syndromes or secondary vasculitis where the underlying etiology of the vasculitis is being driven by infection, malignancy, drug-effect or other. Areas covered This review comprises six individual cases of vasculitis mimics. Each case is presented and the clinical, radiographic, and histological features that distinguish the case from primary vasculitis are highlighted. Key mimics in large, medium and small vessel vasculitis are outlined. Expert opinion The diagnosis of vasculitis requires a comprehensive assessment of clinical, radiographic, and histologic features. Clinicians should be familiar with mimics of primary vasculitis conditions. In the case of non-inflammatory mimics, it is important to differentiate from primary vasculitides in order to avoid unnecessary and potentially harmful immunosuppression. For cases of secondary vasculitis, identification of the correct etiologic cause is critical because treatment of the underlying stimulus is necessary for successful management and outcomes.
Fatigue does not increase limb asymmetry or induce proximal joint power shift in habitual, multi-speed runners

ABSTRACT During prolonged jogging, joint moment and work tend to decrease in the distal (ankle) joint but increase at proximal (hip/knee) joints as performance fatigue manifests, and such adaptations might be expected to occur in sprinting. Fatigue is also thought to increase inter-limb asymmetries, which is speculated to influence injury risk. However, the effects of fatigue on sprint running gait have been incompletely studied, so these hypotheses remain untested. Using statistical parametric mapping, we compared 3-D kinematics and ground reaction force production between the dominant (DL) and non-dominant (NDL) legs of 13 soccer players during both non-fatigued and fatigued sprint running. Contrary to the tested hypotheses, relative between-leg differences were greater in non-fatigued than fatigued sprinting. DL generated higher propulsive impulse due to increased ankle work, while NDL exhibited greater vertical impulse, potentially due to greater hip flexion prior to downward foot acceleration. Whilst few changes were detected in DL once fatigued, NDL shifted towards greater horizontal force production, largely resulting from an increase in plantar flexion (distal-joint) moments and power. After fatiguing running, inter-limb asymmetry was reduced and no distal-to-proximal shift in joint work was detected. These adaptations may attenuate decreases in running speed whilst minimising injury risk.
The scale‐dependent slip pattern for a uniform fault model obeying the rate‐ and state‐dependent friction law

A uniform antiplane fault model obeying the rate‐ and state‐dependent friction law and surrounded by a steady‐slipping region with a constant loading rate is studied through quasi‐dynamic numerical method. Findings indicate that the model exhibits scale‐dependent slip characteristics. Previous studies have demonstrated that the fault slip pattern changes from aseismic creep or slow earthquakes to seismic instabilities as the fault length W increases from around the nucleation size hc to well above hc. In the latter, instabilities typically nucleate periodically from the center of the fault and develop into characteristic events after the whole fault reaches a background stress level. For a fault with larger W/hc, characteristic events nucleate near the boundary or alternatively from both sides before the entire fault returns to background level. As W/hc increases further, additional events with rupture size between hc and W appear. The number of small events is expected to increase with W/hc. The reason these small events do not rupture the whole fault is that the locked region forming on the fault when nucleation occurs acts as a large and low stress barrier. These small events continually create stress concentrations that serve as preparations for the next larger earthquake until the final characteristic event occurs. Meanwhile, the fault in this process gradually evolves into extreme sensitivity that any slight perturbation could change the original slip pattern. Although the current result is far from explaining the observed slip complexity on natural faults, it suggests a trend of increasing slip complexity with W/hc. Therefore, our understanding of the fault behavior may differ from previous knowledge that a relatively uniform and isolated fault model obeying the rate‐ and state‐dependent friction law only exhibits periodic or aperiodic system‐size events.
Depositional Relations of Umpqua and Tyee Formations (Eocene), Southwestern Oregon

Studies of the depositional relations of the Umpqua and Tyee Formations (Eocene) in southwestern Oregon indicate a need for reassessing the correlations and currently used terminology. The Umpqua Formation (as herein restricted) consists of as much as 10,000 ft (3,000 m) of mudstone, sandstone, and conglomerate of nonmarine to deep marine origin. A basaltic basement that underlies the sedimentary rocks in most of the area and was formerly included in the Umpqua is herein considered a separate unit and assigned to the Siletz River Volcanics. A proposal to subdivide the Umpqua into three unconformity-bounded formations (in ascending order: Roseburg, Lookingglass, and Flournoy Formations) in the area west of Roseburg, Oregon, is not recognized in this report because of quest onable correlations and limited extent of some units. Foremost of these questionable correlations is that of the Flournoy Formation with rocks formerly assigned to the Tyee Formation in areas as far north as the latitude of Salem, Oregon. My investigations of depositional facies and lithologic criteria do not substantiate this correlation. The Tyee Formation, which conformably overlies the Umpqua, is a predominantly sandstone unit about 6,000 ft (1,800 m) thick, deposited in environments ranging from shallow marine and nonmarine deltaic on the south, to slope and deep marine basinal to the north. Deposition across the Umpqua-Tyee boundary contact represents a change in tectonic setting from active plate margin of the Umpqua to more stable marginal basin deposition of the Tyee. This change is also reflected in a change in provenance as indicated by the characteristic arkosic and micaceous aspects of Tyee sandstones.
Land, Labor, and Rural Development: Analyzing Participation in India's Village Dairy Cooperatives

Livestock-based livelihoods are currently being promoted by international development agencies as part of global efforts to combat poverty. India's dairy development program, organized around village cooperatives, has become an important model for such efforts. This article aims to identify household characteristics that influence membership in India's rural dairy cooperatives by comparing two villages representing different degrees of success. Utilizing logistic regression methods, data collected through a comprehensive survey of all households in the two villages are analyzed to examine (1) how variables describing animal ownership, agricultural attributes, and household labor availability contribute to explaining membership in the dairy cooperative; and (2) whether factors influencing membership differ across the two villages. Our results indicate that although agricultural property ownership influences cooperative membership in both villages, the kind of dairy animal used and labor utilized for dairying work also have a significant and context-specific effect on household participation.
Collecting Physicians’ Preferences on Medical Devices: Are We Doing It Right? Evidence from Italian Orthopedists Using 2 Different Stated Preference Methods

Objectives Physician preference items (PPIs) are high-cost medical devices for which clinicians express firm preferences with respect to a particular manufacturer or product. This study aims to identify the most important factors in the choice of new PPIs (hip or knee prosthesis) and infer about the existence of possible response biases in using 2 alternative stated preference techniques. Methods Six key attributes with 3 levels each were identified based on a literature review and clinical experts’ opinions. An online survey was administered to Italian hospital orthopedists using type 1 best-worst scaling (BWS) and binary discrete choice experiment (DCE). BWS data were analyzed through descriptive statistics and conditional logit model. A mixed logit regression model was applied to DCE data, and willingness-to-pay (WTP) was estimated. All analyses were conducted using Stata 16. Results A sample of 108 orthopedists were enrolled. In BWS, the most important attribute was “clinical evidence,” followed by “quality of products,” while the least relevant items were “relationship with the sales representative” and “cost. ” DCE results suggested instead that orthopedists prefer high-quality products with robust clinical evidence, positive health technology assessment recommendation and affordable cost, and for which they have a consolidated experience of use and a good relationship with the sales representative. Conclusions The elicitation of preferences for PPIs using alternative methods can lead to different results. The BWS of type 1, which is similar to a ranking exercise, seems to be more affected by acquiescent responding and social desirability than the DCE, which introduces tradeoffs in the choice task and is likely to reveal more about true preferences. Highlights Physician preference items (PPIs) are medical devices particularly exposed to physicians’ choice with regard to type of product and supplier. Some established techniques of collecting preferences can be affected by response biases such as acquiescent responding and social desirability. Discrete choice experiments, introducing more complex tradeoffs in the choice task, are likely to mitigate such biases and reveal true physicians’ preferences for PPIs.
A precipitation dipole in eastern North America

We have identified a dipole in annual precipitation across eastern North America (ENA) east of 100°W between 30°N and 60°N. This dipole appears to create spatially coherent opposing variations in precipitation with a separation of the two regions around 45°N. Annual average precipitation over ENA appears to be stable and unimodal, suggesting that the amount of overall precipitation variability is a small fraction of the mean and is largely determined by similar large scale processes. Analysis of regional average time series at interannual (3–7 year) and decadal (10–16 year) scales indicates that the dipole over the ENA region is most clearly discernible at the decadal scale. Linear regression analysis between global sea surface temperatures (SSTs) and precipitation over the two subregions in ENA suggests that SST variations in several areas of the oceans tend to be associated with opposite precipitation anomalies in the two subregions of ENA.
Large Language Models as Source Planner for Personalized Knowledge-grounded Dialogue

Open-domain dialogue system usually requires different sources of knowledge to generate more informative and evidential responses. However, existing knowledge-grounded dialogue systems either focus on a single knowledge source or overlook the dependency between multiple sources of knowledge, which may result in generating inconsistent or even paradoxical responses. To incorporate multiple knowledge sources and dependencies between them, we propose SAFARI, a novel framework that leverages the exceptional capabilities of large language models (LLMs) in planning, understanding, and incorporating under both supervised and unsupervised settings. Specifically, SAFARI decouples the knowledge grounding into multiple sources and response generation, which allows easy extension to various knowledge sources including the possibility of not using any sources. To study the problem, we construct a personalized knowledge-grounded dialogue dataset \textit{\textbf{K}nowledge \textbf{B}ehind \textbf{P}ersona}~(\textbf{KBP}), which is the first to consider the dependency between persona and implicit knowledge. Experimental results on the KBP dataset demonstrate that the SAFARI framework can effectively produce persona-consistent and knowledge-enhanced responses.
Singular sets on spaces with integral curvature bounds and diffeomorphism finiteness for manifolds

In this paper, we are concerned with noncollapsed Riemannian manifolds $(M^{n},g)$ with integral curvature bounds, as well as their Gromov-Hausdorff limits $(M^{n}_{i},g_{i})\xrightarrow{GH}(X,d)$. Our main result generalizes Cheeger's Hausdorff dimension estimate for the singular set in [7] and improve it into Minkowski dimension estimate in the spirit of Cheeger-Naber [12]. We also prove a difffeomorphism finiteness theorem for manifolds in the critical case, using Cheeger-Naber's methods in [13].