Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental origins of mosaic evolution in the avian cranium

Significance Studies reconstructing morphological evolution have long relied on simple representations of organismal form or on limited sampling of species, hindering a comprehensive understanding of the factors shaping biological diversity. Here, we combine high-resolution 3D quantification of skull shape with dense taxonomic sampling across a major vertebrate clade, birds, to demonstrate that the avian skull is formed of multiple semi-independent regions that epitomize mosaic evolution, with cranial regions and major lineages evolving with distinct rates and modes. We further show that the evolvability of different cranial regions reflects their disparate embryonic origins. Finally, we present a hypothetical reconstruction of the ancestral bird skull using this high-resolution shape data to generate a detailed estimate of extinct forms in the absence of well-preserved three-dimensional fossils. Mosaic evolution, which results from multiple influences shaping morphological traits and can lead to the presence of a mixture of ancestral and derived characteristics, has been frequently invoked in describing evolutionary patterns in birds. Mosaicism implies the hierarchical organization of organismal traits into semiautonomous subsets, or modules, which reflect differential genetic and developmental origins. Here, we analyze mosaic evolution in the avian skull using high-dimensional 3D surface morphometric data across a broad phylogenetic sample encompassing nearly all extant families. We find that the avian cranium is highly modular, consisting of seven independently evolving anatomical regions. The face and cranial vault evolve faster than other regions, showing several bursts of rapid evolution. Other modules evolve more slowly following an early burst. Both the evolutionary rate and disparity of skull modules are associated with their developmental origin, with regions derived from the anterior mandibular-stream cranial neural crest or from multiple embryonic cell populations evolving most quickly and into a greater variety of forms. Strong integration of traits is also associated with low evolutionary rate and low disparity. Individual clades are characterized by disparate evolutionary rates among cranial regions. For example, Psittaciformes (parrots) exhibit high evolutionary rates throughout the skull, but their close relatives, Falconiformes, exhibit rapid evolution in only the rostrum. Our dense sampling of cranial shape variation demonstrates that the bird skull has evolved in a mosaic fashion reflecting the developmental origins of cranial regions, with a semi-independent tempo and mode of evolution across phenotypic modules facilitating this hyperdiverse evolutionary radiation.
The Modal Nature of Structures in Ontic Structural Realism

Ontic structural realism is the view that structures are what is real in the first place in the domain of fundamental physics. The structures are usually conceived as including a primitive modality. However, it has not been spelled out as yet what exactly that modality amounts to. This paper proposes to fill this lacuna by arguing that the fundamental physical structures possess a causal essence, being powers. Applying the debate about causal vs categorical properties in analytic metaphysics to ontic structural realism, I show that the standard argument against categorical and for causal properties holds for structures as well. Structural realism, as a position in the metaphysics of science that is a form of scientific realism, is committed to causal structures. The metaphysics of causal structures is supported by physics, and it can provide for a complete and coherent view of the world that includes all domains of empirical science.
SPITZER IMAGING OF STRONGLY LENSED HERSCHEL-SELECTED DUSTY STAR-FORMING GALAXIES

We present the rest-frame optical spectral energy distribution (SED) and stellar masses of six Herschel-selected gravitationally lensed dusty, star-forming galaxies (DSFGs) at 1 < z < 3. These galaxies were first identified with Herschel/SPIRE imaging data from the Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS) and the Herschel Multi-tiered Extragalactic Survey (HerMES). The targets were observed with Spitzer/IRAC at 3.6 and 4.5 μm. Due to the spatial resolution of the IRAC observations at the level of 2″, the lensing features of a background DSFG in the near-infrared are blended with the flux from the foreground lensing galaxy in the IRAC imaging data. We make use of higher resolution Hubble/WFC3 or Keck/NIRC2 Adaptive Optics imaging data to fit light profiles of the foreground lensing galaxy (or galaxies) as a way to model the foreground components, in order to successfully disentangle the foreground lens and background source flux densities in the IRAC images. The flux density measurements at 3.6 and 4.5 μm, once combined with Hubble/WFC3 and Keck/NIRC2 data, provide important constraints on the rest-frame optical SED of the Herschel-selected lensed DSFGs. We model the combined UV- to millimeter-wavelength SEDs to establish the stellar mass, dust mass, star formation rate, visual extinction, and other parameters for each of these Herschel-selected DSFGs. These systems have inferred stellar masses in the range 8 × 1010–4 × 1011 M⊙ and star formation rates of around 100 M⊙ yr−1. This puts these lensed submillimeter systems well above the SFR-M* relation observed for normal star-forming galaxies at similar redshifts. The high values of SFR inferred for these systems are consistent with a major merger-driven scenario for star formation.
A Bayesian Semiparametric Accelerated Failure Time Model

Summary. A Bayesian semiparametric approach is described for an accelerated failure time model. The error distribution is assigned a Polya tree prior and the regression parameters a noninformative hierarchical prior. Two cases are considered: the first assumes error terms are exchangeable; the second assumes that error terms are partially exchangeable. A Markov chain Monte Carlo algorithm is described to obtain a predictive distribution for a future observation given both uncensored and censored data.
Methods Study Population The black African population consists of Nigerians recruited in the framework of the ongoing Nigerian Population Research on Environment Gene and Health

Emerging epidemiological data indicate that cardiovascular disease is now the major challenge to public health in sub-Saharan Africa. Hypertension, the major risk factor for stroke, heart failure, and chronic kidney disease, is the main driver of this epidemic. Most, although not all, cross-sectional data from different areas of sub-Saharan Africa aimed at evaluating the burden of high blood pressure (BP) defined hypertension solely on the basis of clinic BP. This excludes a substantial number of individuals who have hypertension that is masked to conventional office measurement. Masked hypertension, however, is not an innocuous clinical state as recent outcome studies clearly demonstrated that masked hypertension and sustained hypertension confer similar risks in terms of cardiovascular risk. Abstract—Hitherto, diagnosis of hypertension in sub-Saharan Africa was largely based on conventional office blood pressure (BP). Data on the prevalence of masked hypertension (MH) in this region is scarce. Among individuals with normal office BP (<140/90 mm Hg), we compared the prevalence and determinants of MH diagnosed with self-monitored home blood pressure (≥135/85 mm Hg) among 293 Nigerians with a reference population consisting of 3615 subjects enrolled in the International Database on Home Blood Pressure in Relation to Cardiovascular Outcomes. In the reference population, the prevalence of MH was 14.6% overall and 11.1% and 39.6% in untreated and treated participants, respectively. Among Nigerians, the prevalence standardized to the sex and age distribution of the reference population was similar with rates of 14.4%, 8.6%, and 34.6%, respectively. The mutually adjusted odds ratios of having MH in Nigerians were 2.34 (95% confidence interval, 1.39–3.94) for a 10-year higher age, 1.92 (1.11–3.31) and 1.70 (1.14–2.53) for 10or 5-mm Hg increments in systolic or diastolic office BP, and 3.05 (1.08–8.55) for being on antihypertensive therapy. The corresponding estimates in the reference population were similar with odds ratios of 1.80 (1.62–2.01), 1.64 (1.45–1.87), 1.13 (1.05– 1.22), and 2.84 (2.21–3.64), respectively. In conclusion, MH is as common in Nigerians as in other populations with older age and higher levels of office BP being major risk factors. A significant proportion of true hypertensive subjects therefore remains undetected based on office BP, which is particularly relevant in sub-Saharan Africa, where hypertension is now a major cause of death. (Hypertension. 2016;67:1249-1255. DOI: 10.1161/HYPERTENSIONAHA.116.07242.)
A Dual Role for TNF-α in Type 1 Diabetes: Islet-Specific Expression Abrogates the Ongoing Autoimmune Process When Induced Late but Not Early During Pathogenesis1

We report here that islet-specific expression of TNF-α can play a dual role in autoimmune diabetes, depending on its precise timing in relation to the ongoing autoimmune process. In a transgenic model (rat insulin promoter-lymphocytic choriomeningitis virus) of virally induced diabetes, TNF-α enhanced disease incidence when induced through an islet-specific tetracycline-dependent promoter system early during pathogenesis. Blockade of TNF-α during this phase prevented diabetes completely, suggesting its pathogenetic importance early in disease development. In contrast, TNF-α expression abrogated the autoimmune process when induced late, which was associated with a reduction of autoreactive CD8 lymphocytes in islets and their lytic activities. Thus, the fine-tuned kinetics of an autoreactive process undergo distinct stages that respond in a differential way to the presence of TNF-α. This observation has importance for understanding the complex role of inflammatory cytokines in autoimmunity.
Arterial Stiffness Differences between Aerobically and Resistance Trained Turkish Elite Athletes

Abstract The purpose of this study was to evaluate whether arterial stiffness was different in aerobicallytrained elite athletes than in anaerobically or resistance trained elite athletes. The cohort comprised 36 healthymale volunteers, aged between 17 and 32 years. All subjects were basketball players (n=10), weightlifters (n=11) orsedentary controls (n=15). The Pulse Trace System (Micro Medical Ltd., Rochester, UK) was employed to recordcentral and peripheral arterial stiffness. Echocardiographic images were taken by the use of a commerciallyavailable machine (Vivid 7 GE-Vingmed, Horten, Norway) with a 2.5 MHz transducer. Aortic elastic propertiesderived from echocardiographic measurements did not differ between the groups (p<0.05). Pulse wave velocitymeasurements reflected significantly lower values in both the basketball players and weightlifters compared tocontrols (p<0.001-0.05). No significant difference was seen between the basketball players and weightlifters(p<0.05). Contrary to existing knowledge, arterial stiffness of athletes that perform more resistance exercise suchas weightlifters improved significantly and did not get worse. This result implies that in the long-term arterialstiffness improves with sports activities that are predominantly comprised of resistance exercises despite increasedarterial stiffness in the acute phase.
Nerve Growth Factor Modulation of Retinal Ganglion Cell Physiology

Nerve growth factor (NGF) is an endogenous neurotrophin involved in the development, maintenance and regeneration of mammalian sympathetic and sensory neurons. Additionally, NGF is known to have trophic and differentiating activity on several populations of cholinergic neurons of the central nervous system (CNS), and to act as a differentiation factor in the development of the visual cortex. The paramount functions of NGF in the visual system are also highlighted by the presence of this neurotrophin and both its receptors TrkA and p75 in most intra‐ocular tissues, including lens, vitreous, choroid, iris, and trabecular meshwork. In the retina, NGF is produced and utilized specifically by retinal ganglion cells (RGC), bipolar neurons and glial cells, and is thought to have crucial protective effects in several disease states. Studies on the role of NGF on RGCs survival following optic nerve transection, ischemic injury, ocular hypertension and glaucoma are discussed in this review. J. Cell. Physiol. 229: 1130–1133, 2014. © 2014 Wiley Periodicals, Inc.
MCC/IMS signals in human breath related to sarcoidosis—results of a feasibility study using an automated peak finding procedure

A feasibility study using an ion mobility spectrometer coupled with a multi-capillary column (MCC) was started to identify characteristic peaks of volatile compounds in exhaled human breath samples of 10 ml volume. The breath of 20 patients with sarcoidosis and suspicion of sarcoidosis because of mediastinal lymph node enlargement was investigated. Using a set of procedures for data processing and scoring a sector of interest was determined within the IMS-chromatogram. It could be shown that a procedure related to a single peak in the IMS-chromatogram delivers differentiation into the two groups of patients with confirmed sarcoidosis and those suffering no sarcoidosis. The potential biomarker is characterized by the following parameters: inverse mobility (1/K0) 0.53 ± 0.01 V s cm−2—retention time 22 ± 5 s. These results are a first step in breath analysis by MCC/IMS in patients with sarcoidosis by an automated procedure applied to IMS-chromatograms directly.
Clinical Evaluation of a Skin Protectant for the Management of Incontinence-Associated Dermatitis

PURPOSE: The purpose of this study was to evaluate the efficacy of an investigational skin protectant product at managing severe skin breakdown associated with incontinence. DESIGN: Open-label, nonrandomized, prospective study. SUBJECTS AND SETTING: The sample comprised 16 patients; inclusion criteria were: patients older than 18 years, cared for in the intensive care unit of a level I trauma center hospital or in long-term care facilities in the northeast region of the United States, and had incontinence-associated dermatitis (IAD). Twelve of the patients had epidermal skin loss and 4 had severe redness. METHODS: The investigational product is a formulation based on acrylate chemistry. The skin protectant application schedule was twice weekly for up to 3 weeks for a maximum of 6 applications during the study period. The skin was evaluated via a skin assessment instrument specifically designed for use in this study; this instrument has not undergone validation studies. The main outcome measure was changes in the instrument score over time. In addition, complete reepithelialization was recorded when observed, and pain scores (associated with IAD) were noted in participants who were able to report pain. RESULTS: The IAD score improved in 13 of 16 patients, remained unchanged in 1 patient, and deteriorated in 2 patients. The median percent improvement in the skin assessment instrument was 96% (P = .013). Four of the patients with epidermal skin loss had complete reepithelialization of the skin surface with 4 to 6 applications of the skin protectant, and 5 had substantial improvement. The 4 patients with severe red skin returned to healthy normal skin with 2 to 4 skin protectant applications. Substantial pain reduction was reported by all 9 patients who reported pain at enrollment. No adverse events associated with the skin protectant application were reported during data collection. CONCLUSION: Results of this study suggest that an acrylate-based product, evaluated here for the first time in patients, may be effective as a protective barrier in the presence of continued incontinence. Additional research is needed to confirm these findings.
Direct In Vivo Observation of Transventricular Absorption in the Hydrocephalic Dog Using Magnetic Resonance Imaging

RATIONALE AND OBJECTIVES.A model of chronic noncommunicating hydrocephalus in canines was developed, and gadolinium- DTPA (Gd-DTPA)-enhanccd magnetic resonance imaging, physiologic and morphologic studies were performed to investigate transventricular absorption of cerebrospinal fluid. METHODS.Chronic hydrocephalus was induced in 12 mongrel dogs by injection of a silastic mixture into the prepontine cisterns. Ventricular pressure was measured during the development of hydrocephalus, and lateral ventriculo-ventricular perfusions with Gd-DTPA were performed under controlled conditions during serial magnetic resonance imaging studies. RESULTS.Hydrocephalus developed over an average of 129 ± 24 days after induction, and the intraventricular pressure increased from an initial level of 14 ± 4 cm H2O to a stabilized plateau of 25 ± 5 cm H2O. Increased signal intensity in the brain matter, as seen on magnetic resonance images of chronic hydrocephalic dogs perfused with Gd-DTPA in the lateral ventricles, was consistent with the presence of the contrast agent in the periventricular extracellular space. This increased signal intensity was not observed in control animals. CONCLUSIONS.These results provide direct evidence of transventricular absorption in chronic hydrocephalus.
Bradyrhizobium japonicum NnrR, a Denitrification Regulator, Expands the FixLJ-FixK2 Regulatory Cascade

ABSTRACT In Bradyrhizobium japonicum, a gene named nnrR was identified which encodes a protein with high similarity to FNR/CRP-type transcriptional regulators. Mutant strains carrying an nnrR null mutation were unable to grow anaerobically in the presence of nitrate or nitrite, and they lacked both nitrate and nitrite reductase activities. Anaerobic activation of an nnrR′-′lacZ fusion required FixLJ and FixK2. In turn, N oxide-mediated induction of nir and nor genes encoding nitrite and nitric oxide reductase, respectively, depended on NnrR. Thus, NnrR expands the FixLJ-FixK2 regulatory cascade by an additional control level which integrates the N oxide signal required for maximal induction of the denitrification genes.
Persistently raised C-reactive protein levels are associated with advanced periodontal disease.

OBJECTIVE The aim was to investigate whether there was an association between periodontitis or tooth loss in a homogeneous group of 60-70-year-old Western European men and either a sustained high or low level of C-reactive protein (CRP). MATERIAL AND METHODS Men enrolled in a cohort study of cardiovascular disease in Northern Ireland were screened in 1990-1994 and rescreened in 2001-2004, when a periodontal examination was completed. High-sensitivity CRP was measured from fasting blood samples. There were 806 men with six or more teeth who had either a high level (>3 mg/l) or a lower level of CRP at both time points. Multivariate analysis was carried out using logistic regression with adjustment for possible confounders. Models were constructed with the CRP level as the outcome variable and various measures of periodontal status (low and high threshold periodontitis) or tooth loss as predictor variables. Confounders included in the analysis were known cardiovascular risk factors of age, smoking, diabetes, BMI and socioeconomic status. RESULTS There were 67 men who had a high value of CRP (>3 mg/l) and 739 men who had a CRP value <or=3 mg/l at both time points. The unadjusted odds ratio (OR) for advanced periodontitis to be associated with high CRP was 3.62, p=0.0003. The association was somewhat attenuated but remained significant (OR=2.49, p=0.02) after adjustment for confounders. A high level of tooth loss was also associated with high CRP with an adjusted OR of 2.17, p=0.008. Low threshold periodontitis was not associated with the level of CRP. CONCLUSION There was an association between advanced periodontitis and elevated CRP levels as measured at two time points at a 10-year interval in the 60-70-year-old European males investigated. This association was adjusted for various cardiovascular risk factors. There was also an association between high levels of tooth loss and high CRP in the men studied.
Lossless Compression of Hyperspectral Images Using a Quantized Index to Lookup Tables

We propose an enhancement to the algorithm for lossless compression of hyperspectral images using lookup tables (LUTs). The original LUT method searched the previous band for a pixel of equal value to the pixel colocalized with the one to be predicted. The pixel in the same position as the obtained pixel in the current band is used as a predictor. LUTs were used to speed up the search. The LUT method has also been extended into a method called Locally Averaged Interband Scaling (LAIS)-LUT that uses two LUTs per band. One of the two LUT predictors that is the closest one to the LAIS estimate is chosen as the predictor for the current pixel. We propose the uniform quantization of the colocated pixels before using them for indexing the LUTs. The use of quantization reduces the size of the LUTs by an order of magnitude. The results show that the proposed method outperforms previous methods; a 3% increase in compression efficiency was observed compared to the current state-of-the-art method, LAIS-LUT.
Outcomes Associated With Advanced Nursing Practice Prescriptive Authority

&NA; Thirty‐three advanced practice nurses (APNs) in 25 different primary care sites in one state participated in a study of the safety and effectiveness of APN prescriptive authority. Data were analyzed on 1,708 patients seen during a 2‐month period. Outcomes of care were studied using three different measures as well as patient satisfaction. Evaluation of patient outcome by APN and physician indicated that in 76% of the cases, the patient's condition stabilized or improved. Patients evaluated their own outcomes positively. Participating physicians were unanimous in their evaluation of APN prescriptive authority as beneficial to their patients.