bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of metalloproteins and novel protein folds using variational autoencoders
Authors: Greener Joe G. , Moffat Lewis , Jones David T 
Published: October 2018

AbstractThe design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to biology due to the rise in available data. We attempt to link protein design and deep learning by using variational autoencoders to generate protein sequences conditioned on desired properties. Potential copper and calcium binding sites are added to non-metal binding proteins without human intervention and compared to a hidden Markov model. In another use case, a grammar of protein structures is developed and used to produce sequences for a novel protein topology. One candidate structure is found to be stable by molecular dynamics simulation. The ability of our model to confine the vast search space of protein sequences and to scale easily has the potential to assist in a variety of protein design tasks.
Fault Slip Rates and Seismic Moment Deficits on Major Faults in Ordos Constrained by GPS Observation
Authors: Huang Yilei , Wang Qingliang , Hao Ming , Zhou Shiyong 
Published: October 2018

AbstractThe Ordos Block, surrounded by numerous active faults, is a relatively rigid but dangerous area with many strong historical earthquakes. We derive the block rotation velocity and fault slip rates in this area by using GPS data recorded from 1999 to 2007 and implementing an elastic block model. Instead of assuming vertical faults, as did most previous studies in and around Ordos, we use an improved method to invert for the fault dip angles and construct a closed 3-D fault system in our inversion. The predicted slip rates range from <1 mm/yr to ~ 10 mm/yr. Our results are roughly consistent with geological and other geodetic observations. Using the estimated slip rates, we also calculate the cumulative seismic moment due to fault locking and the released moment from historical earthquake catalogues. A comparison of the two quantities indicates that the Hetao Rift has an unreleased seismic moment equal to a Mw7.9 earthquake, which is also indicated by frequent earthquakes above M6 after 1900.
Observations on spontaneous tumor formation in mice overexpressing mitotic kinesin Kif14
Authors: Sishtla Kamakshi , Pitt Natalie , Shadmand Mehdi , O’Hare Michael N. , Sulaiman Rania S. , Sinn Anthony L. , Condon Keith , Pollok Karen E. , Sandusky George E. , Corson Timothy W. 
Published: October 2018

AbstractThe KIF14 locus is gained and overexpressed in various malignancies, with prognostic relevance. Its protein product, a mitotic kinesin, accelerates growth of normal mammary epithelial cells in vitro and retinoblastoma tumours in a mouse model, while KIF14 knockdown blocks growth of brain, liver, ovarian, breast, prostate, and other tumour cells and xenografts. However, the tumour-initiating effects of Kif14 overexpression have not been studied. We aged a cohort of Kif14-overexpressing transgenic mice and wild-type littermates and documented survival, cause of death, and tumour burden. The Kif14 transgene was expressed in all tissues examined, and was associated with increased proliferation marker expression. Neither mouse weights nor overall survival differed between genotypes. However, Kif14 transgenic mice showed a higher incidence of fatal lymphomas (73 vs. 50%, p = 0.03, Fisher’s exact test), primarily follicular and diffuse B-cell lymphomas. Non-tumour findings included a bilateral ballooning degeneration of lens in 12% of Kif14 transgenic mice but no wild-type mice (p = 0.02). Overall, this work reveals a novel association of Kif14 overexpression with lymphoma but suggests that Kif14 does not have as prominent a role in initiating cancer in other cell types as it does in accelerating tumour development in response to other oncogenic insults.
Characterizing the “sweet spot” for the preservation of a T-cell line using osmolytes
Authors: Pi Chia-Hsing , Yu Guanglin , Petersen Ashley , Hubel Allison 
Published: October 2018

AbstractThis study examined the post-thaw recovery of Jurkat cells cryopreserved in single osmolyte solutions containing sucrose, glycerol or isoleucine, as well as in a combination of the three osmolytes. Cell response was determined using low temperature Raman Spectroscopy and variation in post-thaw recovery with composition was analyzed using statistical modeling. Post-thaw recovery of Jurkat cells in single osmolyte was low. A combination of the osmolytes displayed a non-linear relationship between composition and post-thaw recovery, suggesting that interactions exist between the different solutes. The post-thaw recovery for an optimized multicomponent solution was comparable to that observed using 10% dimethyl sulfoxide and a cooling rate of 1 °C/min. Statistical modeling was used to characterize the importance of each osmolyte in the combination and test for interactions between osmolytes. Higher concentrations of glycerol increase post-thaw recovery and interactions between sucrose and glycerol, as well as sucrose and isoleucine improve post-thaw recovery. Raman images clearly demonstrated that damaging intracellular ice formation was observed more often in the presence of single osmolytes as well as non-optimized multi-component solution compositions.
Umov effect in asteroid (3200) Phaethon
Authors: Zheltobryukhov Maxim , Chornaya Ekaterina , Kochergin Anton , Kornienko Gennady , Matkin Alexey , Ivanova Oleksandra , Luk’yanyk Igor , Zubko Evgenij 
Published: October 2018

Context. The near-Earth asteroid (3200) Phaethon occasionally reveals a comet-like activity. It is a parent body to the Geminid meteor shower and considered as a target for the space mission called Demonstration and Experiment of Space Technology for Interplanetary Voyage Phaethon Flyby Dust Science, DESTINY+.
Aims. We aim to characterize Phaethon through measurements of the degree of linear polarization P measured on Phaethon at large phase angles on its closest approach to Earth on December 17, 2017. These observations allow a more accurate estimation of the maximum value of the degree of linear polarization Pmax of Phaethon, and therefore, of studying the Umov effect.
Methods. We performed polarimetric measurements of Phaethon at large phase angles α and thus constrained its Pmax. We also estimated the geometric albedo a based on the data available in the literature. The obtained Pmax and A were analysed with the Umov effect previously derived for the Moon that establishes an inverse linear correlation between log(Pmax) and log(A) in the lunar regolith.
Results. Our polarimetric observations of Phaethon in the visible reveal the degree of linear polarization P ≈ (17.23 ± 2.00)% at α ≈ 57.9° and P ≈ (31.86 ± 2.00)% at α ≈ 73.2°, which demonstrates no significant wavelength dependence within the error bars of our measurements (± 2%). These data, when combined with what has previously been reported in the literature, suggests at least three types of polarimetric response on Phaethon. For two of them, we infer the maximum linear polarization to be Pmax ≈ 57.9%, occurring at αmax = 131° and Pmax ≈ 44.5% occurring at αmax = 127°. We estimate the geometric albedo (adjusted to α = 3°) to be AR = 0.075 ± 0.007 in the R filter, which appears to be consistent with dark F-type asteroids, as which Phaethon was first classified. We examine the Umov diagrams previously inferred for lunar regolith and find that they are hardly applicable to Phaethon and therefore not to other asteroids either.
The VMC Survey
Authors: Zivkov Viktor , Oliveira Joana M. , Petr-Gotzens Monika G. , Cioni Maria-Rosa L. , Rubele Stefano , van Loon Jacco Th. , Bekki Kenji , Cusano Felice , de Grijs Richard , Ivanov Valentin D. , Marconi Marcella , Niederhofer Florian , Ripepi Vincenzo , Sun Ning-Chen 
Published: October 2018

Context. Detailed studies of intermediate- and low-mass pre-main-sequence (PMS) stars outside the Galaxy have so far been conducted only for small targeted regions harbouring known star formation complexes. The VISTA Survey of the Magellanic Clouds (VMC) provides an opportunity to study PMS populations down to solar masses on a galaxy-wide scale.
Aims. Our goal is to use near-infrared data from the VMC survey to identify and characterise PMS populations down to ∼1 M⊙ across the Magellanic Clouds. We present our colour–magnitude diagram method, and apply it to a ∼1.5 deg2 pilot field located in the Large Magellanic Cloud.
Methods. The pilot field is divided into equal-size grid elements. We compare the stellar population in every element with the population in nearby control fields by creating Ks/(Y−Ks) Hess diagrams; the observed density excesses over the local field population are used to classify the stellar populations.
Results. Our analysis recovers all known star formation complexes in this pilot field (N 44, N 51, N 148, and N 138) and for the first time reveals their true spatial extent. In total, around 2260 PMS candidates with ages ≲10 Myr are found in the pilot field. PMS structures, identified as areas with a significant density excess of PMS candidates, display a power-law distribution of the number of members with a slope of −0.86 ± 0.12. We find a clustering of the young stellar populations along ridges and filaments where dust emission in the far-infrared (FIR) (70 μm–500 μm) is bright. Regions with young populations lacking massive stars show a lower degree of clustering and are usually located in the outskirts of the star formation complexes. At short FIR wavelengths (70 μm,100 μm) we report a strong dust emission increase in regions hosting young massive stars, which is less pronounced in regions populated only by less massive (≲4 M⊙) PMS stars.
Cardiovascular Hemodynamic Changes After Antenatal Corticosteroids in Growth Restricted and Appropriate for Gestational Age Fetuses
Authors: Marchi Laura , Pasquini Lucia , Elvan-Taspinar Ayten , Bilardo Caterina Maddalena 
Published: October 2018

Abstract
Purpose To investigate hemodynamic effects after antenatal corticosteroids (ACS) administration in appropriate for gestational age (AGA) and early growth restricted (GR) fetuses by measurement of Doppler cardiovascular function parameters.
Materials and Methods Prospective cohort study. AGA and GR singleton pregnancies receiving ACS for fetal lung maturation between 24 + 0–33 + 6 weeks were enrolled. Feto-placental vascular hemodynamics were studied by: umbilical artery (UA) pulsatility index (PI), middle cerebral artery (MCA) PI, renal artery (RenA) PI. Cardiac function was evaluated by ductus venosus (DV) PI and by echocardiographic parameters: E to A wave ratios (E/A) and mitral and tricuspid annular plane systolic excursion (MAPSE and TAPSE) for diastolic function, left and right myocardial performance index (MPI) for overall (diastolic and systolic) function. A single operator performed all the measurements at 3 different time points (E): E0 before or within 4 hours of ACS administration (baseline examination), E1 24–48 hours after the first dose and E2 7 days after the second dose of ACS. The values were expressed as z-scores. Pairwise comparisons with paired t-test were performed to compare measurements before and after exposure to ACS.
Results 25 AGA and 20 GR fetuses (mean gestational age: 31 + 1 and 30 + 6, respectively) were included in the analysis. In the AGA group ACS administration was associated with a significant reduction in UA PI. In the GR fetuses ACS temporarily (E0-E1) restored UA-end diastolic flow (EDF) in 6 of 9 fetuses with A/R-EDF (“Return of EDF phenomenon”) and produced a significant increase (worsening) in right MPI (both in E1-E2 and in E0-E2).
Conclusion ACS administration is associated with UA vasodilation in both AGA and GR fetuses and with an increase in right MPI in the latter group. This suggests a worsening in cardiac function in GR fetuses.
Sonographic Bedside Quantification of Pleural Effusion Compared to Computed Tomography Volumetry in ICU Patients
Authors: Teichgräber Ulf , Hackbarth Judith 
Published: October 2018

Abstract To date, the reliability of ultrasound for the quantitative assessment of pleural effusion has been limited. In the following study, an easy and cost-effective bedside ultrasound method was developed and investigated for specific use in the intensive care unit (ICU).
22 patients (median age: 58.5 years, range: 37–88 years, 14 men and 8 women) with a total of 31 pleural effusions were examined in the ICU. The inclusion criterion was complete visualization of the effusion on chest computed tomography (CT). The ultrasound (US) examination was performed less than 6 h after the diagnostic CT scan. The pleural effusion volume was calculated volumetrically from the CT scan data. Within 4.58 +/- 2.87 h after the CT scan, all patients were re-examined with US in the ICU. The fluid crescent's thickness was measured between each intercostal space (ICS) with the patient in a supine position and a 30° inclination of the torso. The US measurements were compared to the calculated CT volumes using regression analysis, resulting in the following formula: V=13.330 x ICS6 (V=volume of the effusion [ml]; ICS6=sonographic measurement of the thickness of the liquid crescent [mm] in the sixth ICS).A significant correlation between the sonographically measured and the CT-calculated volumes was best observed for the sixth ICS (R2=0.589; ICC=0.7469 with p<0.0001 and a 95% CI of 0.5364–0.8705).The sonographic assessment of pleural effusions in a supine position and a 30° inclination of the torso is feasible for the volumetric estimation of pleural effusion. This is especially true for ICU patients with severe primary diseases and orthopnea who are unable to sit upright or lie flat.
Identification of Factors Related to Cases of Benign Paroxysmal Positional Vertigo Refractory to Canalicular Repositioning Maneuvers and Evaluation of the Need for Magnetic Resonance Imaging in their Management: Retrospective Analysis of a Series of 176 Cases
Authors: Carnevale Claudio , Til Pérez Guillermo , Arancibia Tagle Diego , Tomás Barberán Manuel , Sarría Echegaray Pedro 
Published: October 2018

Introduction Benign paroxysmal positional vertigo (BPPV) is the most common form of peripheral vertigo, and, in most cases, it presents a favorable prognosis. The treatment is based on a series of specific canalicular repositioning maneuvers that offer an efficacy close to 100%. Despite this, there are cases that are refractory to treatment, with the persistence of the vertigo symptoms.
Objectives The objective of the present paper is to analyze the factors associated with an increased risk of refractory BPPV and the importance of nuclear magnetic resonance in the study of these patients.
Methods We retrospectively reviewed the cases of 176 patients diagnosed with BPPV in our center. We divided them into two groups: responders and non-responders to the treatment, and analyzed the possible risk factors associated with a higher risk of refractory vertigo. Fischer exact test was used.
Results We found 11 cases refractory to treatment; all of them underwent magnetic resonance imaging (MRI) with gadolinium according to our protocol. Of these, four had an otoneurologic background or pathology, and two other patients presented a multicanal involvement. The difference between the two groups was statistically significant (p < 0.05).
Conclusion Otoneurologic background and multicanal involvement were associated with a higher risk of refractory BPPV. When dealing with a BPPV with persistent symptomatology/nystagmus or with early relapse after an initial improvement, other entities that enter into the differential diagnosis must always be considered. We consider it essential to perform an MRI with gadolinium to rule out cases of BPPV that have a central cause.
The Physiologic and Psychophysical Consequences of Severe-to-Profound Hearing Loss
Authors: Hoover Eric , Souza Pamela 
Published: October 2018

AbstractSubstantial loss of cochlear function is required to elevate pure-tone thresholds to the severe hearing loss range; yet, individuals with severe or profound hearing loss continue to rely on hearing for communication. Despite the impairment, sufficient information is encoded at the periphery to make acoustic hearing a viable option. However, the probability of significant cochlear and/or neural damage associated with the loss has consequences for sound perception and speech recognition. These consequences include degraded frequency selectivity, which can be assessed with tests including psychoacoustic tuning curves and broadband rippled stimuli. Because speech recognition depends on the ability to resolve frequency detail, a listener with severe hearing loss is likely to have impaired communication in both quiet and noisy environments. However, the extent of the impairment varies widely among individuals. A better understanding of the fundamental abilities of listeners with severe and profound hearing loss and the consequences of those abilities for communication can support directed treatment options in this population.
Religions, poverty reduction and global development institutions
Authors: Tomalin Emma 
Published: October 2018

AbstractReligious traditions have always played a central role in supporting those experiencing poverty, through service delivery as well as the provision of spiritual resources that provide mechanisms for resilience at both the individual and community level. However, the fact that religions can be seen to support social structures and practices that contribute towards inequality and conflict, also underscores a role for religious traditions in creating conditions of poverty. While the Western-led modern global development institutions that have emerged since the Second World War have tended to be secular in nature, over the past decade or so there has been an apparent ‘turn to religion’ by these global development institutions, as well as in academic development studies. This reflects the realization that modernization and secularization do not necessarily go together, and that religious values and faith actors are important determinants in the drive to reduce poverty, as well as in structures and practices that underpin it. This paper traces three phases of engagement between religions and global development institutions. In phase one, the ‘pre-secular’ or the ‘integrated phase’ seen during the colonial era, religion and poverty reduction were intimately entwined, with the contemporary global development project being a legacy of this. The second phase is the ‘secular’ or the ‘fragmented’ phase, and relates to the era of the global development industry, which is founded on the normative secularist position that modernization will and indeed should lead to secularization. The third phase is characterized by the ‘turn to religion’ from the early 2000s. Drawing the three phases together and reflecting on the nature of the dynamics within the third phase, the ‘turn to religion’, this paper is underpinned by two main questions. First, what does this mean for the apparent processes of secularization? Is this evidence that they are being reversed and that we are witnessing the emergence of the ‘desecularization of development’ or of a ‘post-secular development praxis’? Second, to what extent are FBOs working in development to be defined as neo-liberalism’s ‘little platoons’—shaped by and instrumentalized to the service of secular neo-liberal social, political and economic systems, or do we need to develop a more sophisticated account that can contribute towards better policy and practice around poverty reduction?
How can we restore the generality of the General Theory?
Authors: Togati Teodoro Dario 
Published: October 2018

AbstractIn this paper, I tackle the key issue raised by Pasinetti, namely why Keynes failed to accomplish his revolution and build a unifying ‘monetary theory of production’ framework. I argue that this occurred because, following his Marshallian background, he adopted an oversimplified view of the structure of theories, a problem which, following Leontief, might be labelled as ‘implicit theorising’ (IT). By making a comparison between the General Theory and standard macroeconomics based on Lakatos’s ‘research programme’ notion, this paper explores IT in a systematic fashion and stresses two key points. First, Keynes did not attack the ‘true’ orthodox postulates but only the conclusions deriving from them. Secondly, he failed to articulate his own research programme effectively. Based on these points, the paper concludes that filling such gaps in Keynes’s theory is the precondition for restoring his generality claim.
Widows, Native Law and the Long Shadow of England in Thirteenth-Century Wales
Authors: Cavell Emma 
Published: October 2018

Abstract
This article examines complex core–periphery relationships in the medieval British Isles and, for the first time, explores the role of elite women in facilitating and shaping those relationships. It takes the advent of English-style dower in native Wales before Wales’s conquest by Edward I of England (1282) as a case-study, and explores the interrelationship between ‘law’ and ‘custom’ in the native legal culture, in order to shed new light on Wales’s relationship with England in the final eighty or so years of Welsh independence. It contends not only that Wales, like other ‘peripheral’ regions of the British Isles, was complicit (however unwittingly) in its own subjection to the English ‘core’, but also that the elite women for whom the dower provisions were made were integral to the very processes of cultural exchange that led to the development of ‘Welsh dower’. While modelled on English common law provisions, Welsh dower—a hybrid phenomenon—was also consistent with Welsh legal norms. By variously turning to the law courts, and employing extra-curial and extra-legal methods of negotiation and redress, the women helped to shape and promote these changes, and to embed them in native Welsh before its final conquest by England. It also makes clear not only that the experiences of Wales in these matters differed from those of other of England’s insular neighbours, such as Ireland, but also that the right of these women to suitable provision was always upheld, no matter how mixed or contested the legal environment.
Johnson, ‘Misargyrus’, and Richard Bathurst
Authors: Dixon Peter , Mannion David , Burgess W G 
Published: October 2018

AbstractFour letters in the Adventurer are currently attributed to Johnson, who allegedly disguised his style so that they could be plausibly ascribed to his friend Richard Bathurst. A stylometric analysis, supported by internal evidence, finds the case for disguise implausible, and suggests that the letters are a collaboration between Johnson and Bathurst.