Miracle-dz/UniFAR-FTUs huggingface dataset:
The More We Search, the More We Find: Discovery of a New Lineage and a New Species Complex in the Genus Asparagopsis

In the past few decades, in the marine realm in particular, the use of molecular tools has led to the discovery of hidden taxonomic diversity, revealing complexes of sister species. A good example is the red algal genus Asparagopsis. The two species (A. armata and A. taxiformis) recognized in this genus have been introduced in many places around the world. Within the nominal species A. taxiformis, previous molecular analyses have uncovered several lineages, suggesting the existence of sister species or subspecies. Although the genus has been well studied in some regions (e.g., the Mediterranean Sea and Hawaii), it remains poorly investigated in others (e.g., South Pacific). Our study mainly focused on these latter areas to clarify lineages and better determine lineage status (i.e., native vs. introduced). A total of 188 specimens were collected from 61 sites, 58 of which had never been sampled before. We sequenced the DNA from samples for three markers and obtained 112 sequences for the chloroplastic RuBisCo spacer, 118 sequences for the nuclear LSU rRNA gene, and 174 for the mitochondrial spacer cox2-3. Phylogenetic analyses using all three markers suggested the existence of two cryptic sister species with the discovery of a new clade within A. armata. This clade was found only in Western Australia, Tasmania and New Zealand, and is thus restricted to a subregional biogeographic unit. We also discovered a new, fifth lineage for A. taxiformis restricted to the South Pacific and Western Australia. Except for this newly described lineage, all other lineages showed a global distribution influenced by introduction events. These results illustrate the difficulty in accurately defining cosmopolitan species. Our findings also highlight the need for targeted (i.e., in poorly studied areas) and geographically extensive sampling efforts when studying taxa that have been introduced globally and that are likely to hide species complexes.
Exploring Crystal Plasticity Via Far-Field 3DXRD

A specimen of Ti-7%Al alloy was subject to tensile deformation in situ at APS 1-ID-C. Within it, a neighborhood containing 20 complete grains was indexed in the annealed state and subsequently tracked at several applied stresses during in situ loading, both preceding and following the macroscopic yield stress. The stress states of each grain were observed to reorient significantly post yield despite the fact that their average remained close to the applied uniaxial stress. To aid in interpreting the experimental results, a virtual realization of the neighborhood was created using a finite element mesh. Each individual grain was represented by ∼ 1000 hexahedral elements. Ensemble averaged resolved shear stresses were calculated over the neighborhood from both the experimental and simulated data. Despite the lack of intra-granular resolution in the experiment – and with the aid of the simulated data – the resolved shear stresses projected on several slip system families are shown to statistically capture the associated critical resolved shear stresses. This important result implies that the far-field 3DXRD method may be applied to the study of specific of slip system activity in embedded neighborhoods of grains subject to thermomechanical processing in situ.
Role of Rostral Fastigial Neurons in Encoding a Body-Centered Representation of Translation in Three Dimensions

Many daily behaviors rely critically on estimates of our body motion. Such estimates must be computed by combining neck proprioceptive signals with vestibular signals that have been transformed from a head- to a body-centered reference frame. Recent studies showed that deep cerebellar neurons in the rostral fastigial nucleus (rFN) reflect these computations, but whether they explicitly encode estimates of body motion remains unclear. A key limitation in addressing this question is that, to date, cell tuning properties have only been characterized for a restricted set of motions across head-re-body orientations in the horizontal plane. Here we examined, for the first time, how 3D spatiotemporal tuning for translational motion varies with head-re-body orientation in both horizontal and vertical planes in the rFN of male macaques. While vestibular coding was profoundly influenced by head-re-body position in both planes, neurons typically reflected at most a partial transformation. However, their tuning shifts were not random but followed the specific spatial trajectories predicted for a 3D transformation. We show that these properties facilitate the linear decoding of fully body-centered motion representations in 3D with a broad range of temporal characteristics from small groups of 5–7 cells. These results demonstrate that the vestibular reference frame transformation required to compute body motion is indeed encoded by cerebellar neurons. We propose that maintaining partially transformed rFN responses with different spatiotemporal properties facilitates the creation of downstream body motion representations with a range of dynamic characteristics, consistent with the functional requirements for tasks such as postural control and reaching. SIGNIFICANCE STATEMENT Estimates of body motion are essential for many daily activities. Vestibular signals are important contributors to such estimates but must be transformed from a head- to a body-centered reference frame. Here, we provide the first direct demonstration that the cerebellum computes this transformation fully in 3D. We show that the output of these computations is reflected in the tuning properties of deep cerebellar rostral fastigial nucleus neurons in a specific distributed fashion that facilitates the efficient creation of body-centered translation estimates with a broad range of temporal properties (i.e., from acceleration to position). These findings support an important role for the rostral fastigial nucleus as a source of body translation estimates functionally relevant for behaviors ranging from postural control to perception.
Innervation of the Face Studied Using Modifications to Sihler’s Technique in a Primate Model

Background: There has been no reliable technique with which to display the innervation within whole-tissue specimens of the face. Such a technique preserves the architecture of the facial muscles and provides new data on intramuscular and sensory neural networks. Sihler’s technique preferentially stains myelinated nerves within whole tissue, which is rendered transparent. On transillumination, entire neural networks can be studied in situ without the need for dissection and histologic examination. The purpose of this study was to apply Sihler’s technique to study innervation patterns of the face, define end points, and improve specimen transillumination. Methods: Eight macaque fascicularis monkeys were studied. The mimetic muscles of the face with intact facial nerve and sensory nerves were harvested as whole tissue composites. Sihler’s technique was modified with formalin fixation before dissection to minimize autolysis of the myelin sheath. Prolonged immersion in glycerin improved tissue transparency. A replica of the skull was made with silicone and a light source embedded to restore three-dimensional configuration and provide transillumination. Results: The facial nerve and sensory nerves were clearly seen up to their terminations in the transparent muscle and soft tissue. Observations were made with regard to the extramuscular and intramuscular innervation patterns of the facial nerve and sensory nerve patterns. Conclusions: Sihler’s technique is a simple and reliable method with which to study the innervation of the face. This process may be applied to the human face to provide a much-needed roadmap to surgery, and the primate model may be developed for the study of facial reinnervation, facial reanimation, and dynamic facial transplantation.
Psychological and Physical Workload and the Development of Musculoskeletal Symptoms Among Female Elderly-Care Workers

The aim of the present study was to investigate the relations between psychological and physical workload and musculoskeletal neck, shoulder and upper back symptoms. In this longitudinal two-phase cohort study a survey was con- ducted among non-managerial female elderly-care workers (n = 553). The analyses were based on respondents who were considered free from the respective symptoms at initial ratings, resulting in study samples of n = 230 for neck symptoms, n = 211 for shoulder symptoms, n = 400 for upper back symptoms, and n = 204 for low back symptoms. The results indi- cate that psychological workload is related to the development of musculoskeletal (neck and upper back) symptoms measured at an 18-month follow-up, both in itself and in combination with physical workload. The most important finding was that psychological workload shows significant temporal relations to neck and upper back symptoms.
The role of stress mindset in shaping cognitive, emotional, and physiological responses to challenging and threatening stress

ABSTRACT Background and objectives: Prior research suggests that altering situation-specific evaluations of stress as challenging versus threatening can improve responses to stress. The aim of the current study was to explore whether cognitive, physiological and affective stress responses can be altered independent of situation-specific evaluations by changing individuals’ mindsets about the nature of stress in general. Design: Using a 2 × 2 design, we experimentally manipulated stress mindset using multi-media film clips orienting participants (N = 113) to either the enhancing or debilitating nature of stress. We also manipulated challenge and threat evaluations by providing positive or negative feedback to participants during a social stress test. Results: Results revealed that under both threat and challenge stress evaluations, a stress-is-enhancing mindset produced sharper increases in anabolic (“growth”) hormones relative to a stress-is-debilitating mindset. Furthermore, when the stress was evaluated as a challenge, a stress-is-enhancing mindset produced sharper increases in positive affect, heightened attentional bias towards positive stimuli, and greater cognitive flexibility, whereas a stress-is-debilitating mindset produced worse cognitive and affective outcomes. Conclusions: These findings advance stress management theory and practice by demonstrating that a short manipulation designed to generate a stress-is-enhancing mindset can improve responses to both challenging and threatening stress.
Workplace Status: The Development and Validation of a Scale

Research suggests that employee status, and various status proxies, relate to a number of meaningful outcomes in the workplace. The advancement of the study of status in organizational settings has, however, been stymied by the lack of a validated workplace status measure. The purpose of this manuscript, therefore, is to develop and validate a measure of workplace status based on a theoretically grounded definition of status in organizations. Subject-matter experts were used to examine the content validity of the measure. Then, 2 separate samples were employed to assess the psychometric properties (i.e., factor structure, reliability, convergent and discriminant validity) and nomological network of a 5-item, self-report Workplace Status Scale (WSS). To allow for methodological flexibility, an additional 3 samples were used to extend the WSS to coworker reports of a focal employee’s status, provide additional evidence for the validity and reliability of the WSS, and to demonstrate consensus among coworker ratings. Together, these studies provide evidence of the psychometric soundness of the WSS for assessing employee status using either self-reports or other-source reports. The implications of the development of the WSS for the study of status in organizations are discussed, and suggestions for future research using the new measure are offered.
Intra- and Interspecific Differences in Diet Quality and Composition in a Large Herbivore Community

Species diversity in large herbivore communities is often explained by niche segregation allowed by differences in body mass and digestive morphophysiological features. Based on large number of gut samples in fall and winter, we analysed the temporal dynamics of diet composition, quality and interspecific overlap of 4 coexisting mountain herbivores. We tested whether the relative consumption of grass and browse differed among species of different rumen types (moose-type and intermediate-type), whether diet was of lower quality for the largest species, whether we could identify plant species which determined diet quality, and whether these plants, which could be “key-food-resources” were similar for all herbivores. Our analyses revealed that (1) body mass and rumen types were overall poor predictors of diet composition and quality, although the roe deer, a species with a moose-type rumen was confirmed as an “obligatory non grazer”, while red deer, the largest species, had the most lignified diet; (2) diet overlap among herbivores was well predicted by rumen type (high among species of intermediate types only), when measured over broad plant groups, (3) the relationship between diet composition and quality differed among herbivore species, and the actual plant species used during winter which determined the diet quality, was herbivore species-specific. Even if diets overlapped to a great extent, the species-specific relationships between diet composition and quality suggest that herbivores may select different plant species within similar plant group types, or different plant parts and that this, along with other behavioural mechanisms of ecological niche segregation, may contribute to the coexistence of large herbivores of relatively similar body mass, as observed in mountain ecosystems.
Portuguese Community Pharmacists' Attitudes to and Knowledge of Antibiotic Misuse: Questionnaire Development and Reliability

Objective To develop and evaluate the reliability of a self-administered questionnaire designed to assess the attitudes and knowledge of community pharmacists in Portugal about microbial resistance and the antibiotic dispensing process. Methods This study was divided into the following three stages: (1) design of the questionnaire, which included a literature review and a qualitative study with focus-group sessions; (2) assessment of face and content validity, using a panel of experts and a pre-test of community pharmacists; and, (3) pilot study and reliability analysis, which included a test-retest study covering fifty practising pharmacists based at community pharmacies in five districts situated in Northern Portugal. Questionnaire reproducibility was quantified using the intraclass correlation coefficient (ICC; 95% confidence interval) computed by means of one-way analysis of variance (ANOVA). Internal consistency was evaluated using Cronbach's alpha. Results The correlation coefficients were fair to good (ICC>0.4) for all statements (scale-items) regarding knowledge of and attitudes to antibiotic resistance, and ranged from fair to good to excellent for statements about situations in which pharmacists acknowledged that antibiotics were sometimes dispensed without a medical prescription (ICC>0.8). Cronbach's alpha for this section was 0.716. Conclusions The questionnaire designed in this study is valid and reliable in terms of content validity, face validity and reproducibility.
Enhanced Hypothalamic NMDA Receptor Activity Contributes to Hyperactivity of HPA Axis in Chronic Stress in Male Rats

Chronic stress stimulates corticotrophin-releasing hormone (CRH)-expressing neurons in the paraventricular nucleus (PVN) of the hypothalamus and leads to hypothalamic-pituitary-adrenal (HPA) axis hyperactivity, but the mechanisms underlying this action are unknown. Because chronic stress enhances N-methyl-d-aspartate receptor (NMDAR) activity in various brain regions, we hypothesized that augmented NMDAR activity contributes to the hyperactivity of PVN-CRH neurons and the HPA axis in chronic stress. We performed whole-cell patch-clamp recordings on PVN-CRH neurons expressing CRH promoter-driven enhanced green fluorescent protein in brain slices from rats exposed to chronic unpredictable mild stress (CUMS) and unstressed rats. CUMS rats had significantly higher expression levels of the NMDAR subunits GluN1 in the PVN than unstressed rats. Furthermore, puff NMDA-elicited currents, evoked NMDAR currents, and the baseline frequency of the miniature excitatory postsynaptic currents (mEPSCs) in PVN-CRH neurons were significantly larger in CUMS rats than in unstressed rats. The NMDAR-specific antagonist 2-amino-5-phosphonopentanoic acid (AP5) significantly decreased the frequency of mEPSCs of PVN-CRH neurons in CUMS rats but did not change the frequency or amplitude of mEPSCs in unstressed rats. Bath application of AP5 normalized the elevated firing activity of PVN-CRH neurons in CUMS rats but not in unstressed rats. In addition, microinjection of the NMDAR antagonist memantine into the PVN normalized the elevated corticosterone (CORT) levels in CUMS rats to the levels in unstressed rats, but did not alter CORT levels in unstressed rats. Our findings suggest that synaptic NMDAR activity is enhanced in CUMS rats and contributes to the hyperactivity of PVN-CRN neurons and the HPA axis.
Early Spring, Severe Frost Events, and Drought Induce Rapid Carbon Loss in High Elevation Meadows

By the end of the 20th century, the onset of spring in the Sierra Nevada mountain range of California has been occurring on average three weeks earlier than historic records. Superimposed on this trend is an increase in the presence of highly anomalous “extreme” years, where spring arrives either significantly late or early. The timing of the onset of continuous snowpack coupled to the date at which the snowmelt season is initiated play an important role in the development and sustainability of mountain ecosystems. In this study, we assess the impact of extreme winter precipitation variation on aboveground net primary productivity and soil respiration over three years (2011 to 2013). We found that the duration of snow cover, particularly the timing of the onset of a continuous snowpack and presence of early spring frost events contributed to a dramatic change in ecosystem processes. We found an average 100% increase in soil respiration in 2012 and 2103, compared to 2011, and an average 39% decline in aboveground net primary productivity observed over the same time period. The overall growing season length increased by 57 days in 2012 and 61 days in 2013. These results demonstrate the dependency of these keystone ecosystems on a stable climate and indicate that even small changes in climate can potentially alter their resiliency.
Deep-Sequencing Method for Quantifying Background Abundances of Symbiodinium Types: Exploring the Rare Symbiodinium Biosphere in Reef-Building Corals

The capacity of reef-building corals to associate with environmentally-appropriate types of endosymbionts from the dinoflagellate genus Symbiodinium contributes significantly to their success at local scales. Additionally, some corals are able to acclimatize to environmental perturbations by shuffling the relative proportions of different Symbiodinium types hosted. Understanding the dynamics of these symbioses requires a sensitive and quantitative method of Symbiodinium genotyping. Electrophoresis methods, still widely utilized for this purpose, are predominantly qualitative and cannot guarantee detection of a background type below 10% of the total Symbiodinium population. Here, the relative abundances of four Symbiodinium types (A13, C1, C3, and D1) in mixed samples of known composition were quantified using deep sequencing of the internal transcribed spacer of the ribosomal RNA gene (ITS-2) by means of Next Generation Sequencing (NGS) using Roche 454. In samples dominated by each of the four Symbiodinium types tested, background levels of the other three types were detected when present at 5%, 1%, and 0.1% levels, and their relative abundances were quantified with high (A13, C1, D1) to variable (C3) accuracy. The potential of this deep sequencing method for resolving fine-scale genetic diversity within a symbiont type was further demonstrated in a natural symbiosis using ITS-1, and uncovered reef-specific differences in the composition of Symbiodinium microadriaticum in two species of acroporid corals (Acropora digitifera and A. hyacinthus) from Palau. The ability of deep sequencing of the ITS locus (1 and 2) to detect and quantify low-abundant Symbiodinium types, as well as finer-scale diversity below the type level, will enable more robust quantification of local genetic diversity in Symbiodinium populations. This method will help to elucidate the role that background types have in maximizing coral fitness across diverse environments and in response to environmental change.
Taming of the monitors: reducing false alarms in intensive care units

False alarms in intensive care units represent a serious threat to patients. We propose a method for detection of five live-threatening arrhythmias. It is designed to work with multimodal data containing electrocardiograph and arterial blood pressure or photoplethysmograph signals. The presented method is based on descriptive statistics and Fourier and Hilbert transforms. It was trained using 750 records. The method was validated during the follow-up phase of the CinC/Physionet Challenge 2015 on a hidden dataset with 500 records, achieving a sensitivity of 93% (95%) and a specificity of 87% (88%) for real-time (retrospective) files. The given sensitivity and specificity resulted in score of 81.62 (84.96) for real-time (retrospective) records. The presented method is an improved version of the original algorithm awarded the first and the second prize in CinC/Physionet Challenge 2015.
Amplification and protein overexpression of cyclin D1: Predictor of occult nodal metastasis in early oral cancer

Accurate nodal staging is pivotal for treatment planning in early (stage I–II) oral cancer. Unfortunately, current imaging modalities lack sensitivity to detect occult nodal metastases. Chromosomal region 11q13, including genes CCND1, Fas‐associated death domain (FADD), and CTTN, is often amplified in oral cancer with nodal metastases. However, evidence in predicting occult nodal metastases is limited.