Miracle-dz/UniFAR-FTUs huggingface dataset:
The extracranial venous system in the heads of beaked whales, with implications on diving physiology and pathogenesis

Beaked whales are a poorly known but diverse group of whales that have received considerable attention due to strandings that have been temporally and spatially associated with naval sonar deployment. Postmortem studies on stranded carcasses have revealed lesions consistent with decompression sickness, including intravascular gas and fat emboli. These findings have been supported by analyses of intravascular gas emboli showing composition dominated by nitrogen gas. To increase our understanding of the pathophysiology of nitrogen bubble formation and intravascular embolization, we examined the gross and microscopic anatomy of the venous system in the head of beaked whales. Since the potential sources of intravascular fat and gas emboli were of greatest interest, focus was placed on the acoustic fat bodies and pneumatic accessory sinus system. Herein, we describe intimate arteriovenous associations with specialized adipose depots and air sinuses in beaked whales. These vascular structures comprise an extensive network of thin‐walled vessels with a large surface area, which is likely to facilitate exchange of nitrogen gas and may, therefore, form anatomic regions that may be important in physiological management of diving gases. These structures may also be vulnerable to pathologic introduction of emboli into the vascular system. Expansive, thin‐walled venous lakes are found within the pterygoid region, which suggest the potential for nitrogen exchange as well as for compensation of middle‐ear pressures during descent on a dive. These findings warrant further research into the structure and function of this morphology as it relates to normal and pathologic physiology. J. Morphol. 277:34–64, 2016. © 2015 Wiley Periodicals, Inc.
PINK1 regulates mitochondrial trafficking in dendrites of cortical neurons through mitochondrial PKA

Mitochondrial Protein Kinase A (PKA) and PTEN‐induced kinase 1 (PINK1), which is linked to Parkinson's disease, are two neuroprotective serine/threonine kinases that regulate dendrite remodeling and mitochondrial function. We have previously shown that PINK1 regulates dendrite morphology by enhancing PKA activity. Here, we show the molecular mechanisms by which PINK1 and PKA in the mitochondrion interact to regulate dendrite remodeling, mitochondrial morphology, content, and trafficking in dendrites. PINK1‐deficient cortical neurons exhibit impaired mitochondrial trafficking, reduced mitochondrial content, fragmented mitochondria, and a reduction in dendrite outgrowth compared to wild‐type neurons. Transient expression of wild‐type, but not a PKA‐binding‐deficient mutant of the PKA‐mitochondrial scaffold dual‐specificity A Kinase Anchoring Protein 1 (D‐AKAP1), restores mitochondrial trafficking, morphology, and content in dendrites of PINK1‐deficient cortical neurons suggesting that recruiting PKA to the mitochondrion reverses mitochondrial pathology in dendrites induced by loss of PINK1. Mechanistically, full‐length and cleaved forms of PINK1 increase the binding of the regulatory subunit β of PKA (PKA/RIIβ) to D‐AKAP1 to enhance the autocatalytic‐mediated phosphorylation of PKA/RIIβ and PKA activity. D‐AKAP1/PKA governs mitochondrial trafficking in dendrites via the Miro‐2/TRAK2 complex and by increasing the phosphorylation of Miro‐2. Our study identifies a new role of D‐AKAP1 in regulating mitochondrial trafficking through Miro‐2, and supports a model in which PINK1 and mitochondrial PKA participate in a similar neuroprotective signaling pathway to maintain dendrite connectivity.
Recent Incidence of Trisomy 21 in a Japanese Hospital

Trisomy 21, the chromosome abnormality responsible for over 95% of Down syndrome, is one of the most common conditions encountered in the genetic clinic. Recently, the increasing share of pregnancies with advanced maternal age and its impact on the increased incidence of trisomy 21 have been reported in the United States [1-3]. Our hospital is one of main perinatal centers in Tokyo, Japan (about 2,100 deliveries per year). In this study, we examined the recent incidence of trisomy 21 associated with maternal age at our hospital. We reviewed the obstetric records of all Japanese singleton pregnancies at our hospital form January 2005 through January 2011. Demographic information and the characteristics of labor were extracted from patient charts. The conditions of the study patients were Japanese singleton pregnancies whose estimated date of delivery were from January 2006 through December 2011 and managed from 14 weeks or earlier at our hospital. In this study, thus, we have excluded the cases as follows (1) multifetal pregnancies, (2) non-Japanese pregnancies, (3) the time of first visit of our hospital at ≥ 15 weeks’ gestation, and/or (4) spontaneous fetal demise before 22 weeks’ gestation. We examined the maternal age at age of the estimated date of delivery. There were 28 cases of trisomy 21 in 10964 Japanese singleton pregnancies (1/392). In our hospital, there were 39 cases of trisomy 21 in total during this period; however, there were 8 cases of trisomy 21 refereed to our hospital at ≥ 15 weeks’ gestation due to fetal abnormality, 2 non-Japanese cases of trisomy 21 and 1 case of trisomy 21 in twin pregnancy. During this period, the average maternal age of all pregnancies was 32.3 ± 5.5 years old and 35% of the mothers were 35 years old or more at the estimated date of delivery; while the average maternal age in the cases with trisomy 21 was 38.0 ± 4.7 years old. The incidence of trisomy 21 in cases of maternal age of < 35 years (3 cases, average: 27.7 ± 3.5 years), 35 39 years (15 cases, average: 37.5 ± 1.1 years) and ≥ 40 years (10 cases, average: 41.7 ± 1.9 years) were 1/2364, 1/209 and 1/74, respectively. These incidences by maternal age were almost similar to those reported previously in the United States [4]. Of the 28 cases of trisomy 21, 11 cases (39%) were diagnosed as trisomy 21 prenatally using amniocentesis due to maternal request. Ten cases of them (91%) were artificial aborted; thus, the incidence of live births with trisomy 21 was 1/608 (18 cases). The average maternal age in the cases diagnosed prenatally was significant higher than that diagnosed postnatelly (40.1 ± 3.3 vs. 36.6 ± 5.0 years, p < 0.01 by unpaired t-test). The tendency is also similar to that reported in the United States [1-3]. In conclusion, in Japan the recent increased share of pregnancies with advanced maternal age seemed to contribute to the increased incidence of trisomy 21 as observed in other countries.
PRMT1 regulates astrocytic differentiation of embryonic neural stem/precursor cells

Arginine methylation is a post‐translational modification which is catalyzed by protein arginine methyltransferases (PRMTs). Here, we report that PRMT1 is highly expressed in neural stem/precursor cells (NS/PCs) of mouse embryos, and knockdown of PRMT1 in NS/PCs suppresses the generation of astrocytes. The luciferase assay demonstrated that knockdown of PRMT1 inhibits activation of the promoter of a typical astrocytic marker gene, glial fibrillary acidic protein (Gfap), in NS/PCs. The transcription factor signal transducer and activator of transcription 3 (STAT3) is known to generally be critical for astrocytic differentiation of NS/PCs. We found that PRMT1 methylates arginine residue(s) of STAT3 to regulate its activity positively, resulting in the promotion of astrocytic differentiation of NS/PCs.
Convergence of macroscopic tongue anatomy in ruminants and scaling relationships with body mass or tongue length

Various morphological measures demonstrate convergent evolution in ruminants with their natural diet, in particular with respect to the browser/grazer dichotomy. Here, we report quantitative macroanatomical measures of the tongue (length and width of specific parts) of 65 ruminant species and relate them to either body mass (BM) or total tongue length, and to the percentage of grass in the natural diet (%grass). Models without and with accounting for the phylogenetic structures of the dataset were used, and models were ranked using Akaike's Information Criterion. Scaling relationships followed geometric principles, that is, length measures scaled with BM to the power of 0.33. Models that used tongue length rather than BM as a body size proxy were consistently ranked better, indicating that using size proxies that are less susceptible to a wider variety of factors (such as BM that fluctuates with body condition) should be attempted whenever possible. The proportion of the freely mobile tongue tip of the total tongue (and hence also the corpus length) was negatively correlated to %grass, in accordance with concepts that the feeding mechanism of browsers requires more mobile tongues. It should be noted that some nonbrowsers, such as cattle, use a peculiar mechanism for grazing that also requires long, mobile tongues, but they appear to be exceptions. A larger corpus width with increasing %grass corresponds to differences in snout shape with broader snouts in grazers. The Torus linguae is longer with increasing %grass, a finding that still warrants functional interpretation. This study shows that tongue measures covary with diet in ruminants. In contrast, the shape of the tongue (straight or “hourglass‐shaped” as measured by the ratio of the widest and smallest corpus width) is unrelated to diet and is influenced strongly by phylogeny. J. Morphol. 277:351–362, 2016. © 2015 Wiley Periodicals, Inc.
BGO as a hybrid scintillator / Cherenkov radiator for cost-effective time-of-flight PET

Due to detector developments in the last decade, the time-of-flight (TOF) method is now commonly used to improve the quality of positron emission tomography (PET) images. Clinical TOF-PET systems based on L(Y)SO:Ce crystals and silicon photomultipliers (SiPMs) with coincidence resolving times (CRT) between 325 ps and 400 ps FWHM have recently been developed. Before the introduction of L(Y)SO:Ce, BGO was used in many PET systems. In addition to a lower price, BGO offers a superior attenuation coefficient and a higher photoelectric fraction than L(Y)SO:Ce. However, BGO is generally considered an inferior TOF-PET scintillator. In recent years, TOF-PET detectors based on the Cherenkov effect have been proposed. However, the low Cherenkov photon yield in the order of ∼10 photons per event complicates energy discrimination–a severe disadvantage in clinical PET. The optical characteristics of BGO, in particular its high transparency down to 310 nm and its high refractive index of ∼2.15, are expected to make it a good Cherenkov radiator. Here, we study the feasibility of combining event timing based on Cherenkov emission with energy discrimination based on scintillation in BGO, as a potential approach towards a cost-effective TOF-PET detector. Rise time measurements were performed using a time-correlated single photon counting (TCSPC) setup implemented on a digital photon counter (DPC) array, revealing a prompt luminescent component likely to be due to Cherenkov emission. Coincidence timing measurements were performed using BGO crystals with a cross-section of 3 mm × 3 mm and five different lengths between 3 mm and 20 mm, coupled to DPC arrays. Non-Gaussian coincidence spectra with a FWHM of 200 ps were obtained with the 27 mm3 BGO cubes, while FWHM values as good as 330 ps were achieved with the 20 mm long crystals. The FWHM value was found to improve with decreasing temperature, while the FWTM value showed the opposite trend.
An exploration of clients' goals during inpatient and outpatient stroke rehabilitation

Aims The purpose of this pilot study was to explore the goal setting of clients with stroke during inpatient and outpatient rehabilitation. Methods Sixteen participants were recruited from an inpatient (n=6) and outpatient (n=10) stroke rehabilitation programme. A semi-structured interview was conducted to determine participant's goals for rehabilitation and the goals of therapy sessions. Responses were coded according to the International Classification of Functioning, Disability and Health and thematic analysis undertaken to further summarize the responses. Findings Thematic analysis identified a difference in the types of goals identified by the two participant groups. Goals for the inpatient group were focused on activities and participation (n=18, 78%), whereas a more even distribution between activities and participation (n=23, 56%) or body functions and structures (n=18, 44%) was observed with the outpatient group. When asked to identify the perceived goals of therapy session, participants from bot.
Nervous system development in the fairy shrimp Branchinella sp. (Crustacea: Branchiopoda: Anostraca): Insights into the development and evolution of the branchiopod brain and its sensory organs

Using immunohistochemical labeling against acetylated a‐tubulin and serotonin in combination with confocal laser scanning microscopy and 3D‐reconstruction, we investigated the temporary freshwater pond inhabitant Branchinella sp. (Crustacea: Branchiopoda: Anostraca) for the first time to provide detailed data on the development of the anostracan nervous system. Protocerebral sense organs such as the nauplius eye and frontal filament organs are present as early as the hatching stage L0. In the postnaupliar region, two terminal pioneer neurons grow from posterior to anterior to connect the mandibular neuromeres. The first protocerebral neuropil to emerge is not part of the central complex but represents the median neuropil, and begins to develop from L0+ onwards. In stage L3, the first evidence of developing compound eyes is visible. This is followed by the formation of the visual neuropils and the neuropils of the central complex in the protocerebrum. From the deutocerebral lobes, the projecting neuron tract proceeds to both sides of the lateral protocerebrum, forming a chiasma just behind the central body. In the postnaupliar region, the peripheral nervous system, commissures and connectives develop along an anterior–posterior gradient after the fasciculation of the terminal pioneer neurons with the mandibular neuromere. The peripheral nervous system in the thoracic segments consists of two longitudinal neurite bundles on each side which connect the intersegmental nerves, together with the ventral nervous system forming an orthogon‐like network. Here, we discuss, among other things, the evidence of a fourth nauplius eye nerve and decussating projecting neuron tract found in Branchinella sp. , and provide arguments to support our view that the crustacean frontal filament (organ) and onychophoran primary antenna are homologous. J. Morphol. 277:1423–1446, 2016. © 2016 Wiley Periodicals, Inc.
Fully automated treatment planning for head and neck radiotherapy using a voxel-based dose prediction and dose mimicking method

Recent works in automated radiotherapy treatment planning have used machine learning based on historical treatment plans to infer the spatial dose distribution for a novel patient directly from the planning image. We present a probabilistic, atlas-based approach which predicts the dose for novel patients using a set of automatically selected most similar patients (atlases). The output is a spatial dose objective, which specifies the desired dose-per-voxel, and therefore replaces the need to specify and tune dose-volume objectives. Voxel-based dose mimicking optimization then converts the predicted dose distribution to a complete treatment plan with dose calculation using a collapsed cone convolution dose engine. In this study, we investigated automated planning for right-sided oropharaynx head and neck patients treated with IMRT and VMAT. We compare four versions of our dose prediction pipeline using a database of 54 training and 12 independent testing patients by evaluating 14 clinical dose evaluation criteria. Our preliminary results are promising and demonstrate that automated methods can generate comparable dose distributions to clinical. Overall, automated plans achieved an average of 0.6% higher dose for target coverage evaluation criteria, and 2.4% lower dose at the organs at risk criteria levels evaluated compared with clinical. There was no statistically significant difference detected in high-dose conformity between automated and clinical plans as measured by the conformation number. Automated plans achieved nine more unique criteria than clinical across the 12 patients tested and automated plans scored a significantly higher dose at the evaluation limit for two high-risk target coverage criteria and a significantly lower dose in one critical organ maximum dose. The novel dose prediction method with dose mimicking can generate complete treatment plans in 12–13 min without user interaction. It is a promising approach for fully automated treatment planning and can be readily applied to different treatment sites and modalities.
Histone deactylase gene expression profiles are associated with outcomes in blunt trauma patients

BACKGROUND Treatment with histone deacetylase (HDAC) inhibitors, such as valproic acid, increases survival in animal models of trauma and sepsis. Valproic acid is a pan-inhibitor that blocks most of the known HDAC isoforms. Targeting individual HDAC isoforms may increase survival and reduce complications, but little is known of the natural history of HDAC gene expression following trauma. We hypothesized that distinct HDAC isoform gene expression patterns would be associated with differences in outcomes following trauma. METHODS Twenty-eight–day longitudinal HDAC leukocyte gene expression profiles in 172 blunt trauma patients were extracted from the Inflammation and the Host Response to Injury (Glue Grant) data set. Outcome was classified as complicated (death or no recovery by Day 28, n = 51) or uncomplicated (n = 121). Mixed modeling was used to compare the HDAC expression trajectories between the groups, corrected for Injury Severity Score (ISS), base deficit, and volume of blood products transfused during the initial 12 hours following admission. Weighted gene correlation network analysis identified modules of genes with significant coexpression, and HDAC genes were mapped to these modules. Biologic function of these modules was investigated using the Gene Ontology database. RESULTS Elevated longitudinal HDAC expression trajectories for HDAC1, HDAC3, HDAC6, and HDAC11 were associated with complicated outcomes. In contrast, suppressed expression of Sirtuin 3 (SIRT3) was associated with adverse outcome (p < 0.01). Weighted gene correlation network analysis identified significant coexpression of HDAC and SIRT genes with genes involved in ribosomal function and down-regulation of protein translation in response to stress (HDAC1), T-cell signaling, and T-cell selection (HDAC3) as well as coagulation and hemostasis (SIRT3). No coexpression of HDAC11 was identified. CONCLUSION Expression trajectories of HDAC1, HDAC3, HDAC6, HDAC11, and SIRT3 correlate with outcomes following trauma and may potentially serve as biomarkers. They may also be promising targets for pharmacologic intervention. The effects of HDAC and SIRT gene expression in trauma may be mediated through pathways involved in ribosomal and T-cell function as well as coagulation and hemostasis. LEVEL OF EVIDENCE Prognostic study, level III.
The vocal sac of Hylodidae (Amphibia, Anura): Phylogenetic and functional implications of a unique morphology

Anuran vocal sacs are elastic chambers that recycle exhaled air during vocalizations and are present in males of most species of frogs. Most knowledge of the diversity of vocal sacs relates to external morphology; detailed information on internal anatomy is available for few groups of frogs. Frogs of the family Hylodidae, which is endemic to the Atlantic Forest of Brazil and adjacent Argentina and Paraguay, have three patterns of vocal sac morphology—that is, single, subgular; paired, lateral; and absent. The submandibular musculature and structure of the vocal sac mucosa (the internal wall of the vocal sac) of exemplar species of this family and relatives were studied. In contrast to previous accounts, we found that all species of Crossodactylus and Hylodes possess paired, lateral vocal sacs, with the internal mucosa of each sac being separate from the contralateral one. Unlike all other frogs for which data are available, the mucosa of the vocal sacs in these genera is not supported externally by the mm. intermandibularis and interhyoideus. Rather, the vocal sac mucosa projects through the musculature and is free in the submandibular lymphatic sac. The presence of paired, lateral vocal sacs, the internal separation of the sac mucosae, and their projection through the m. interhyoideus are synapomorphies of the family. Furthermore, the specific configuration of the m. interhyoideus allows asymmetric inflation of paired vocal sacs, a feature only reported in species of these diurnal, stream‐dwelling frogs.
The ontogeny of the olfactory system in ceratophryid frogs (Anura, Ceratophryidae)

The aquatic‐to‐terrestrial shift in the life cycle of most anurans suggests that the differences between the larval and adult morphology of the nose are required for sensory function in two media with different physical characteristics. However, a better controlled test of specialization to medium is to compare adult stages of terrestrial frogs with those that remain fully aquatic as adults. The Ceratophryidae is a monophyletic group of neotropical frogs whose diversification from a common terrestrial ancestor gave rise to both terrestrial (Ceratophrys, Chacophrys) and aquatic (Lepidobatrachus) adults. So, ceratophryids represent an excellent model to analyze the morphology and possible changes related to a secondary aquatic life. We describe the histomorphology of the nose during the ontogeny of the Ceratophryidae, paying particular attention to the condition in adult stages of the recessus olfactorius (a small area of olfactory epithelium that appears to be used for aquatic olfaction) and the eminentia olfactoria (a raised ridge on the floor of the principal cavity correlated with terrestrial olfaction). The species examined (Ceratophrys cranwelli, Chacophrys pierottii, Lepidobatrachus laevis, and L. llanensis) share a common larval olfactory organ composed by the principal cavity, the vomeronasal organ and the lateral appendix. At postmetamorphic stages, ceratophryids present a common morphology of the nose with the principal, middle, and inferior cavities with characteristics similar to other neobatrachians at the end of metamorphosis. However, in advanced adult stages, Lepidobatrachus laevis presents a recessus olfactorius with a heightened (peramorphic) development and a rudimentary (paedomorphic) eminentia olfactoria. Thus, the adult nose in Lepidobatrachus laevis arises from a common developmental ‘terrestrial’ pathway up to postmetamorphic stages, when its ontogeny leads to a distinctive morphology related to the evolutionarily derived, secondarily aquatic life of adults of this lineage.