Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying the World's Most Climate Change Vulnerable Species: A Systematic Trait-Based Assessment of all Birds, Amphibians and Corals

Climate change will have far-reaching impacts on biodiversity, including increasing extinction rates. Current approaches to quantifying such impacts focus on measuring exposure to climatic change and largely ignore the biological differences between species that may significantly increase or reduce their vulnerability. To address this, we present a framework for assessing three dimensions of climate change vulnerability, namely sensitivity, exposure and adaptive capacity; this draws on species’ biological traits and their modeled exposure to projected climatic changes. In the largest such assessment to date, we applied this approach to each of the world’s birds, amphibians and corals (16,857 species). The resulting assessments identify the species with greatest relative vulnerability to climate change and the geographic areas in which they are concentrated, including the Amazon basin for amphibians and birds, and the central Indo-west Pacific (Coral Triangle) for corals. We found that high concentration areas for species with traits conferring highest sensitivity and lowest adaptive capacity differ from those of highly exposed species, and we identify areas where exposure-based assessments alone may over or under-estimate climate change impacts. We found that 608–851 bird (6–9%), 670–933 amphibian (11–15%), and 47–73 coral species (6–9%) are both highly climate change vulnerable and already threatened with extinction on the IUCN Red List. The remaining highly climate change vulnerable species represent new priorities for conservation. Fewer species are highly climate change vulnerable under lower IPCC SRES emissions scenarios, indicating that reducing greenhouse emissions will reduce climate change driven extinctions. Our study answers the growing call for a more biologically and ecologically inclusive approach to assessing climate change vulnerability. By facilitating independent assessment of the three dimensions of climate change vulnerability, our approach can be used to devise species and area-specific conservation interventions and indices. The priorities we identify will strengthen global strategies to mitigate climate change impacts.
Guideline : Mechanical Ventilation in Adult Patients with Acute Respiratory Distress Syndrome

Eddy Fan, Lorenzo Del Sorbo, Ewan C. Goligher, Carol L. Hodgson, Laveena Munshi, Allan J. Walkey, Neill K. J. Adhikari, Marcelo B. P. Amato, Richard Branson, Roy G. Brower, Niall D. Ferguson, Ognjen Gajic, Luciano Gattinoni, Dean Hess, Jordi Mancebo, Maureen O. Meade, Daniel F. McAuley, Antonio Pesenti, V. Marco Ranieri, Gordon D. Rubenfeld, Eileen Rubin, Maureen Seckel, Arthur S. Slutsky, Daniel Talmor, B. Taylor Thompson, Hannah Wunsch, Elizabeth Uleryk, Jan Brozek, and Laurent J. Brochard; on behalf of the American Thoracic Society, European Society of Intensive Care Medicine, and Society of Critical Care Medicine
Conjugative Plasmid Transfer in Xylella fastidiosa Is Dependent on tra and trb Operon Functions

ABSTRACT The insect-transmitted plant pathogen Xylella fastidiosa is capable of efficient horizontal gene transfer (HGT) and recombination. Natural transformation occurs at high rates in X. fastidiosa, but there also is evidence that certain strains of X. fastidiosa carry native plasmids equipped with transfer and mobilization genes, suggesting conjugation as an additional mechanism of HGT in some instances. Two operons, tra and trb, putatively encoding a conjugative type IV secretion system, are found in some but not all X. fastidiosa isolates, often on native plasmids. X. fastidiosa strains that carry the conjugative transfer genes can belong to different subspecies and frequently differ in host ranges. Using X. fastidiosa strain M23 (X. fastidiosa subsp. fastidiosa) or Dixon (X. fastidiosa subsp. multiplex) as the donor strain and Temecula (X. fastidiosa subsp. fastidiosa) as the recipient strain, plasmid transfer was characterized using the mobilizable broad-host-range vector pBBR5pemIK. Transfer of plasmid pBBR5pemIK was observed under in vitro conditions with both donor strains and was dependent on both tra and trb operon functions. A conjugative mechanism likely contributes to gene transfer between diverse strains of X. fastidiosa, possibly facilitating adaptation to new environments or different hosts. IMPORTANCE Xylella fastidiosa is an important plant pathogen worldwide, infecting a wide range of different plant species. The emergence of new diseases caused by X. fastidiosa, or host switching of existing strains, is thought to be primarily due to the high frequency of HGT and recombination in this pathogen. Transfer of plasmids by a conjugative mechanism enables movement of larger amounts of genetic material at one time, compared with other routes of gene transfer such as natural transformation. Establishing the prevalence and functionality of this mechanism in X. fastidiosa contributes to a better understanding of HGT, adaptation, and disease emergence in this diverse pathogen.
A phase detection scheme for clock and data recovery applications

This paper presents the design and functional simulation of a new multi-level bang-bang phase detector for use in a clock and data recovery circuit (CDR). The designed phase detector provides information of the nature of the delay between its input signals in a digitised manner, establishing six levels of quantisation. To avoid the metastability that hinders the performance of traditional bang-bang phase detectors, a scheme of phase delay sensing is proposed that eliminates the need to sample the data stream close to data transitions in the locked state. Behavioural simulations are provided comparing the performance of the proposed phase detector with that of a conventional bang-bang phase detector.
Butyrophilin controls milk fat globule secretion

The molecular mechanism underlying milk fat globule secretion in mammary epithelial cells ostensibly involves the formation of complexes between plasma membrane butyrophilin and cytosolic xanthine oxidoreductase. These complexes bind adipophilin in the phospholipid monolayer of milk secretory granules, the precursors of milk fat globules, enveloping the nascent fat globules in a layer of plasma membrane and pinching them off the cell. However, using freeze-fracture immunocytochemistry, we find these proteins in locations other than those previously inferred. Significantly, butyrophilin in the residual plasma membrane of the fat globule envelope is concentrated in a network of ridges that are tightly apposed to the monolayer derived from the secretory granule, and the ridges coincide with butyrophilin labeling in the globule monolayer. Therefore, we propose that milk fat globule secretion is controlled by interactions between plasma membrane butyrophilin and butyrophilin in the secretory granule phospholipid monolayer rather than binding of butyrophilin–xanthine oxidoreductase complexes to secretory granule adipophilin.
Sympathetic Voltage-Independent Regulation of Voltage- Gated Calcium Channels in Pancreatic β-Cells

Voltage-gated calcium (CaV) channels are regulated by G proteins via voltage-dependent and independent pathways. Voltage-independent regulation of calcium channels is important for intracellular calcium concentration and insulin secretion. Voltage dependence of each pathway can be elucidated by a prepulse facilitation protocol. Using this experimental approach, we compared CaV regulation by GTPγS and noradrenaline (NA) in rat pancreatic β-cells and rat superior cervical ganglion (SCG) neurons. The SCG neuron is a model in which the bases of CaV channel regulation by G proteins have been established. CaV channel regulation through activation of the sympathetic nervous system has been poorly studied in native insulin-secreting cells. We recorded CaV channel currents by means of the patch-clamp technique in the whole-cell configuration. We found that application of both GTPγS (a nonspecific activator of G proteins) by cell dialysis and noradrenaline (NA)-exposure reduced CaV current amplitude in pancreatic β-cells and in SCG neurons. However, the inhibition of CaV channel currents in GTPγS-dialyzed SCG neurons was relieved by a strong depolarizing pulse. By contrast, in pancreatic β-cells, the inhibition was maintained after a strong depolarizing pulse. In SCG neurons, the CaV channel inhibition by NA is predominantly voltage-dependent, whereas in pancreatic β-cells it is only 40%. Thus, it appears that CaV channels in rat pancreatic β-cells are regulated mainly through a voltage-independent pathway. The signaling pathway for CaV channel regulation by NA in pancreatic β-cells appears to differ from the classic signaling pathway described in SCG neurons. Therefore, voltage-independent regulation of Ca2+ entry through CaV channels is a critical step in understanding the pathophysiology of type 2 diabetes.
Imaging of HCC—Current State of the Art

Early diagnosis of hepatocellular carcinoma (HCC) is crucial for optimizing treatment outcome. Ongoing advances are being made in imaging of HCC regarding detection, grading, staging, and also treatment monitoring. This review gives an overview of the current international guidelines for diagnosing HCC and their discrepancies as well as critically summarizes the role of magnetic resonance imaging (MRI) and computed tomography (CT) techniques for imaging in HCC. The diagnostic performance of MRI with nonspecific and hepatobililiary contrast agents and the role of functional imaging with diffusion-weighted imaging will be discussed. On the other hand, CT as a fast, cheap and easily accessible imaging modality plays a major role in the clinical routine work-up of HCC. Technical advances in CT, such as dual energy CT and volume perfusion CT, are currently being explored for improving detection, characterization and staging of HCC with promising results. Cone beam CT can provide a three-dimensional analysis of the liver with tumor and vessel characterization comparable to cross-sectional imaging so that this technique is gaining an increasing role in the peri-procedural imaging of HCC treated with interventional techniques.
Epigenetic Landscape of Kaposi's Sarcoma-Associated Herpesvirus Genome in Classic Kaposi's Sarcoma Tissues

Kaposi's sarcoma-associated herpesvirus (KSHV) is etiologically related to Kaposi's sarcoma (KS), primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). It typically displays two different phases in its life cycle, the default latency and occasional lytic replication. The epigenetic modifications are thought to determine the fate of KSHV infection. Previous studies elegantly depicted epigenetic landscape of latent viral genome in in vitro cell culture systems. However, the physiologically relevant scenario in clinical KS tissue samples is unclear. In the present study, we established a protocol of ChIP-Seq for clinical KS tissue samples and mapped out the epigenetic landscape of KSHV genome in classic KS tissues. We examined AcH3 and H3K27me3 histone modifications on KSHV genome, as well as the genome-wide binding sites of latency associated nuclear antigen (LANA). Our results demonstrated that the enriched AcH3 was mainly restricted at latent locus while H3K27me3 was widespread on KSHV genome in classic KS tissues. The epigenetic landscape at the region of vIRF3 gene confirmed its silenced state in KS tissues. Meanwhile, the abundant enrichment of LANA at the terminal repeat (TR) region was also validated in the classic KS tissues, however, different LANA binding sites were observed on the host genome. Furthermore, we verified the histone modifications by ChIP-qPCR and found the dominant repressive H3K27me3 at the promoter region of replication and transcription activator (RTA) in classic KS tissues. Intriguingly, we found that the TR region in classic KS tissues was lacking in AcH3 histone modifications. These data now established the epigenetic landscape of KSHV genome in classic KS tissues, which provides new insights for understanding KSHV epigenetics and pathogenesis.
In vitro activity of zoliflodacin (ETX0914) against macrolide-resistant, fluoroquinolone-resistant and antimicrobial-susceptible Mycoplasma genitalium strains

Background Mycoplasma genitalium is estimated to be the second most common cause of bacterial sexually transmitted infection in Europe. It is of increasing public health concern due to the rapid development of resistance to different antimicrobial classes, including the preferred first- and second-line treatments azithromycin and moxifloxacin. Thus, new antimicrobial agents are urgently needed, especially for the treatment of MDR strains. Methods The in vitro activity of the new spiropyrimidinetrione zoliflodacin against 47 M. genitalium strains was assessed by growing M. genitalium in Vero cell culture and measuring growth by quantitative PCR. The collection included 34 moxifloxacin-susceptible (MIC <1 mg/L) and 13 moxifloxacin-resistant (MIC ≥1 mg/L) strains. Twenty-three of the strains were azithromycin resistant (MIC ≥16 mg/L) and 12 of these strains were MDR. Results Only one (2.1%) strain with substantially increased MIC (4 mg/L) and potential resistance to zoliflodacin was found. Zoliflodacin was overall more potent than moxifloxacin (P = 0.009) and no cross-resistance was observed between the two drug classes of topoisomerase II inhibitors. Differences in the MICs of zoliflodacin and azithromycin were not statistically significant; however, 23 (48.9%) compared with potentially 1 (2.1%) of the strains were resistant to azithromycin and zoliflodacin, respectively. Conclusions Zoliflodacin is a promising candidate for the treatment of M. genitalium and it is important to further develop and evaluate this drug.
Digoxin : a model for hypothalamic regulation of neuronal transmission, endocrine function, immunity and cytodifferentiation.

The case report of a family with coexistence of schizophrenia, systemic malignancy, Parkinson's disease, rheumatoid arthritis and syndrome X is described. The coexistence of malignant transformation, neuronal degeneration, immune dysfunction and psychiatric manifestation have been extensively documented in literature. It is possible that a central dysfunction in neuroendocrine and immune integration may play a role in the pathophysiology of these diseases. Elevated levels of an endogenous sodium-potassium ATPase inhibitor, digoxin, a steroidal glycoside, has been reported in syndrome X. The human hypothalamus is the principal source of digoxin. Serum digoxin level and RBC sodium-potassium ATPase were measured in the members of the index family and8 groups of patients with CNS gliomas, Parkinson's disease, motor neuron disease, CNS vasculitis, multiple sclerosis, primary generalised epilepsy, schizophrenia and the acquired immunodeficiency syndrome. Digoxin, being a isoprenoidal compound, its synthesis was assessed by HMG CoA reductase activity. The levels of serum digoxin and HMG CoA reductase activity were found to be increased in the members of the index family and all the 8 groups studied with a corresponding reduction in RBC sodium-potassium ATPase activity. The role of hypothalamic digoxin in the pathogenesis of these diseases is discussed. A digoxin model for hypothalamic regulation of neuronal transmission, endocrine function, immunity and cytodifferentiation is proposed.
Investigating the Effect of Relative Time Delay on Companion Screen Experiences

Mobile devices are increasingly used while watching television, leading to the development of companion apps that complement the content of programmes. A concern for these applications is the extent to which companion app and television content need to be temporally aligned for live synchronisation. In this study, 18 participants watched a nature programme while being shown companion content on a tablet. Temporal synchronisation of content between the devices was varied. Participants completed questionnaires measuring immersion and affect and were tested on their recall for companion app content. While there were no statistically significant effects on these measures, qualitative interviews with participants after viewing consistently revealed that longer 10s delays in content synchronisation were frustrating. This suggests that poor content synchronisation can produce a negative companion experience for viewers and should be avoided.
cGMP in mouse rods: the spatiotemporal dynamics underlying single photon responses

Vertebrate vision begins when retinal photoreceptors transduce photons into electrical signals that are then relayed to other neurons in the eye, and ultimately to the brain. In rod photoreceptors, transduction of single photons is achieved by a well-understood G-protein cascade that modulates cGMP levels, and in turn, cGMP-sensitive inward current. The spatial extent and depth of the decline in cGMP during the single photon response (SPR) have been major issues in phototransduction research since the discovery that single photons elicit substantial and reproducible changes in membrane current. The spatial profile of cGMP decline during the SPR affects signal gain, and thus may contribute to reduction of trial-to-trial fluctuations in the SPR. Here we summarize the general principles of rod phototransduction, emphasizing recent advances in resolving the spatiotemporal dynamics of cGMP during the SPR.
A Review of Visual Representations of Physiologic Data

Background Physiological data is derived from electrodes attached directly to patients. Modern patient monitors are capable of sampling data at frequencies in the range of several million bits every hour. Hence the potential for cognitive threat arising from information overload and diminished situational awareness becomes increasingly relevant. A systematic review was conducted to identify novel visual representations of physiologic data that address cognitive, analytic, and monitoring requirements in critical care environments. Objective The aims of this review were to identify knowledge pertaining to (1) support for conveying event information via tri-event parameters; (2) identification of the use of visual variables across all physiologic representations; (3) aspects of effective design principles and methodology; (4) frequency of expert consultations; (5) support for user engagement and identifying heuristics for future developments. Methods A review was completed of papers published as of August 2016. Titles were first collected and analyzed using an inclusion criteria. Abstracts resulting from the first pass were then analyzed to produce a final set of full papers. Each full paper was passed through a data extraction form eliciting data for comparative analysis. Results In total, 39 full papers met all criteria and were selected for full review. Results revealed great diversity in visual representations of physiological data. Visual representations spanned 4 groups including tabular, graph-based, object-based, and metaphoric displays. The metaphoric display was the most popular (n=19), followed by waveform displays typical to the single-sensor-single-indicator paradigm (n=18), and finally object displays (n=9) that utilized spatiotemporal elements to highlight changes in physiologic status. Results obtained from experiments and evaluations suggest specifics related to the optimal use of visual variables, such as color, shape, size, and texture have not been fully understood. Relationships between outcomes and the users’ involvement in the design process also require further investigation. A very limited subset of visual representations (n=3) support interactive functionality for basic analysis, while only one display allows the user to perform analysis including more than one patient. Conclusions Results from the review suggest positive outcomes when visual representations extend beyond the typical waveform displays; however, there remain numerous challenges. In particular, the challenge of extensibility limits their applicability to certain subsets or locations, challenge of interoperability limits its expressiveness beyond physiologic data, and finally the challenge of instantaneity limits the extent of interactive user engagement.
Selective Emitters in Passivated Emitter and Rear Silicon Solar Cells Enabling 20% on Large Area p-Type Silicon

We present a comparison of solar cells featuring homogeneous and selective emitters on devices with passivated surfaces. Solar cells are fabricated on high quality float zone silicon and commercial Czochralski grown silicon substrates. Three different emitter structures are compared, two homogenous ones and one selective emitter. The surfaces are passivated by a thin thermal oxide. The cells feature screen printed metallization and laser fired point contacts on the rear side. Higher conversion efficiencies are found for the cells with a selective emitter. A gain in the open circuit voltage of up to 1.3% is observed for the cells on FZ-Si. This advantage is smaller on the Cz-Si substrates and the recombination active boron oxygen complex further reduces the profit of the selective emitter in fill factor, open circuit voltage and thus conversion efficiency.
Multi-pass large strain rolling of as-cast AZ31 magnesium alloy

As-cast AZ31 magnesium alloy subjected to multi-pass large strain rolling was investigated. A successive rolling process up to three passes was carried out at 370°C with a pass reduction of 30%. Deformation microstructure characteristics prove that the dynamic recrystallisation (DRX) mode changed with the increase of rolling passes. In the first pass, DRX related to twinning played a dominant role. But in the third pass, DRX grains mainly appeared around the pre-existing grain boundaries. The ultimate strength and elongation of rolled sheets after three passes rolling are enhanced by 37 and 39%, respectively, compared to the as-cast alloy. Meanwhile, the tensile fracture mode was ductile fracture which was different from the ductile–brittle fracture of as-cast.
Developmental and Evolutionary Significance of the Zygomatic Bone

The zygomatic bone is derived evolutionarily from the orbital series. In most modern mammals the zygomatic bone forms a large part of the face and usually serves as a bridge that connects the facial skeleton to the neurocranium. Our aim is to provide information on the contribution of the zygomatic bone to variation in midfacial protrusion using three samples; humans, domesticated dogs, and monkeys. In each case, variation in midface protrusion is a heritable trait produced by one of three classes of transmission: localized dysmorphology associated with single gene dysfunction, selective breeding, or long‐term evolution from a common ancestor. We hypothesize that the shape of the zygomatic bone reflects its role in stabilizing the connection between facial skeleton and neurocranium and consequently, changes in facial protrusion are more strongly reflected by the maxilla and premaxilla. Our geometric morphometric analyses support our hypothesis suggesting that the shape of the zygomatic bone has less to do with facial protrusion. By morphometrically dissecting the zygomatic bone we have determined a degree of modularity among parts of the midfacial skeleton suggesting that these components have the ability to vary independently and thus can evolve differentially. From these purely morphometric data, we propose that the neural crest cells that are fated to contribute to the zygomatic bone experience developmental cues that distinguish them from the maxilla and premaxilla. The spatiotemporal and molecular identity of the cues that impart zygoma progenitors with their identity remains an open question that will require alternative data sets. Anat Rec, 299:1616–1630, 2016. © 2016 The Authors The Anatomical Record Published by Wiley Periodicals, Inc.