bluuebunny/crossref_metadata_2025 huggingface dataset:
NEW INSIGHTS ON THE ROLE OF ENVIRONMENTAL DYNAMICS SHAPING SOUTHERN MESOPOTAMIA: FROM THE PRE-UBAID TO THE EARLY ISLAMIC PERIOD
Authors: Altaweel Mark , Marsh Anke , Jotheri Jaafar , Hritz Carrie , Fleitmann Dominik , Rost Stephanie , Lintner Stephen F. , Gibson McGuire , Bosomworth Matthew , Jacobson Matthew , Garzanti Eduardo , Limonta Mara , Radeff Giuditta
Published: July 2019

Recent fieldwork and archival sedimentary materials from southern Iraq have revealed new insights into the environment that shaped southern Mesopotamia from the pre-Ubaid (early Holocene) until the early Islamic period. These data have been combined with northern Iraqi speleothem, or stalagmite, data that have revealed relevant palaeoclimate information. The new results are investigated in light of textual sources and satellite remote sensing work. It is evident that areas south of Baghdad, and to the region of Uruk, were already potentially habitable between the eleventh and early eighth millennia B.C., suggesting there were settlements in southern Iraq prior to the Ubaid. Date palms, the earliest recorded for Iraq, are evident before 10,000 B.C., and oak trees are evident south of Baghdad in the early Holocene but disappeared after the mid-sixth millennium B.C. New climate results suggest increased aridity after the end of the fourth millennium B.C. For the third millennium B.C. to first millennium A.D., a negative relationship between grain and date palm cultivation in Nippur is evident, suggesting shifting cultivation emphasising one of these crops at any given time in parts of the city. The Shatt en-Nil was also likely used as a channel for most of Nippur's historical occupation from the third millennium B.C. to the first millennium A.D. In the early to mid-first millennium A.D., around the time of the Sasanian period, a major increase in irrigation is evident in plant remains, likely reflecting large-scale irrigation expansion in the Nippur region. The first millennium B.C. to first millennium A.D. reflects a relatively dry period with periodic increased rainfall. Sedimentary results suggest the Nahrawan, prior to it becoming a well-known canal, formed an ancient branch of the Tigris, while the region just south of Baghdad, around Dalmaj, was near or part of an ancient confluence of the Tigris and Euphrates.
Assessment of inner–outer interactions in the urban boundary layer using a predictive model
Authors: Blackman Karin , Perret Laurent , Mathis Romain
Published: July 2019

Urban-type rough-wall boundary layers developing over staggered cube arrays with plan area packing density, $\unicode[STIX]{x1D706}_{p}$, of 6.25 %, 25 % or 44.4 % have been studied at two Reynolds numbers within a wind tunnel using hot-wire anemometry (HWA). A fixed HWA probe is used to capture the outer-layer flow while a second moving probe is used to capture the inner-layer flow at 13 wall-normal positions between $1.25h$ and $4h$ where $h$ is the height of the roughness elements. The synchronized two-point HWA measurements are used to extract the near-canopy large-scale signal using spectral linear stochastic estimation and a predictive model is calibrated in each of the six measurement configurations. Analysis of the predictive model coefficients demonstrates that the canopy geometry has a significant influence on both the superposition and amplitude modulation. The universal signal, the signal that exists in the absence of any large-scale influence, is also modified as a result of local canopy geometry suggesting that although the nonlinear interactions within urban-type rough-wall boundary layers can be modelled using the predictive model as proposed by Mathis et al. (J. Fluid Mech., vol. 681, 2011, pp. 537–566), the model must be however calibrated for each type of canopy flow regime. The Reynolds number does not significantly affect any of the model coefficients, at least over the limited range of Reynolds numbers studied here. Finally, the predictive model is validated using a prediction of the near-canopy signal at a higher Reynolds number and a prediction using reference signals measured in different canopy geometries to run the model. Statistics up to the fourth order and spectra are accurately reproduced demonstrating the capability of the predictive model in an urban-type rough-wall boundary layer.
Analysis of Electromagnetohydrodynamic Stagnation Point Flow of Nanofluid Over a Nonlinear Stretching Sheet with Variable Thickness
Authors: Seth G. S. , Mandal P. K.
Published: July 2019

Present study explores stagnation point flow of nanofluid towards a nonlinear stretching sheet of variable thickness in the presence of electromagnetic field and convective heating. The effect of viscous dissipation and Joule heating are also taken into consideration. Novel concept of non-linear radiative heat flux is also considered. The nanofluid is inspired by Lorentz force which is instigated from the interaction of magnetic and electric fields. Using similarity transformation, the governing partial differential equations are transformed into a system of coupled nonlinear ordinary differential equations and then solved numerically by fourth order Runge-Kutta method along with shooting technique. The velocity, temperature and nanoparticle concentration profiles are plotted and analysed corresponding to various pertinent flow parameters. Also, the skin friction and rate of heat and mass transfers at the surface are computed and explained in detail. It is observed that higher wall thickness parameter results in the reduction of velocity, temperature and nanoparticle concentration when velocity power index is less than unity and opposite effect is observed when velocity power index is greater than unity. Due to intensification of electric field, nanofluid velocity is getting retarded and thereby resulting in enhancement of fluid temperature and nanoparticle concentration.
Contesting Probation in Scotland: How An Agonistic Perspective Travels
Authors: McNeill Fergus
Published: July 2019

In this Review Essay, I try to rise to one of the challenges that Goodman, Page, and Phelps pose to other scholars in their book, Breaking the Pendulum (2017). They invite us to explore whether and how well their “agonistic perspective” on penal change travels. In response, I draw on original archival and oral history research on probation history in Scotland to explore their model’s utility in the context of this particular and challenging test case. Although Scotland is often discussed as an anomaly because of a supposed consensus around an enduring commitment to penal welfarism, my analysis reveals precisely the kinds of contestation that Goodman, Page, and Phelps describe. I conclude that their agonistic perspective seems to travel well, at least to this Atlantic edge of Europe, but that scholars in other jurisdictions will need either to undertake or revisit primary research to properly test the model and further refine it.
INTEGRAL CLOSURE OF STRONGLY GOLOD IDEALS
Authors: CIUPERCĂ CĂTĂLIN
Published: July 2019

We prove that the integral closure of a strongly Golod ideal in a polynomial ring over a field of characteristic zero is strongly Golod, positively answering a question of Huneke. More generally, the rational power $I_{\unicode[STIX]{x1D6FC}}$ of an arbitrary homogeneous ideal is strongly Golod for $\unicode[STIX]{x1D6FC}\geqslant 2$ and, if $I$ is strongly Golod, then $I_{\unicode[STIX]{x1D6FC}}$ is strongly Golod for $\unicode[STIX]{x1D6FC}\geqslant 1$. We also show that all the coefficient ideals of a strongly Golod ideal are strongly Golod.
FINITE -GROUPS ALL OF WHOSE NONNORMAL SUBGROUPS HAVE BOUNDED NORMAL CORES
Authors: YANG DONGFANG , AN LIJIAN , LV HENG
Published: July 2019

Given a positive integer $m$, a finite $p$-group $G$ is called a $BC(p^{m})$-group if $|H_{G}|\leq p^{m}$ for every nonnormal subgroup $H$ of $G$, where $H_{G}$ is the normal core of $H$ in $G$. We show that $m+2$ is an upper bound for the nilpotent class of a finite $BC(p^{m})$-group and obtain a necessary and sufficient condition for a $p$-group to be of maximal class. We also classify the $BC(p)$-groups.
Metaphors and other slippery creatures
Authors: Strick James E.
Published: July 2019

What are cells? How are they related to each other and to the organism as a whole? These questions have exercised biology since Schleiden and Schwann (1838–1839) first proposed cells as the key units of structure and function of all living things. But how do we try to understand them? Through new technologies like the achromatic microscope and the electron microscope. But just as importantly, through the metaphors our culture has made available to biologists in different periods and places. These two new volumes provide interesting history and philosophy of the development of cell biology. Reynolds surveys the field's changing conceptual structure by examining the varied panoply of changing metaphors used to conceptualize and explain cells – from cells as empty boxes, as building blocks, to individual organisms, to chemical factories, and through many succeeding metaphors up to one with great currency today: cells as social creatures in communication with others in their community. There is some of this approach in theVisionsedited collection as well. But this collection also includes rich material on the technologies used to visualize cells and their dialectical relationship with the epistemology of the emerging distinct discipline of cell biology. This volume centres on, but is not limited to, ‘reflections inspired by [E.V.] Cowdry's [1924 volume]General Cytology’; it benefits from a conference on the Cowdry volume as well as a 2011 Marine Biological Lab/Arizona State University workshop on the history of cell biology.
A DELICATE BRIDEGROOM:HABROSUNĒIN SAPPHO, FR. 115V
Authors: Ragusa Giuliana , Rosenmeyer Patricia A.
Published: July 2019

In Sappho's two-line fragment 115V, an unidentified speaker addresses a lucky bridegroom, wondering how best to describe him; the answer follows immediately:τίῳ σ᾿, ὦ φίλε γάμβρε, καλῶς ἐικάσδω;ὄρπακι βραδίνῳ σε μάλιστ᾿ ἐικάσδω.Dear bridegroom, to what do I best compare you?I compare you most of all to a delicate branch.
ARABIC SUPPORT FOR AN EMENDATION OF PLATO,LAWS666B
Authors: Moseley Geoffrey J.
Published: July 2019

AtLeg.666b7, Burnet's emendation of the transmitted λήθην to λήθῃ has been widely accepted. Newly discovered support for this emendation comes from an Arabic version or adaptation of Plato'sLaws, most likely Galen'sSynopsis, quoted by the polymath Abū-Rayḥān al-Bīrūnī (a.d.973–1048) asKitāb al-Nawāmīs li-Aflāṭunin his ethnographic work on India. I transliterate and translate the passage below, proposing two incidental emendations to the Arabic:

wa-qāla l-aṯīniyyu fī l-maqālati l-tāniyati mina l-kitābi: lammā raḥima [sic proraḥimati] l-ālihatu ǧinsa l-bašari min aǧli annahū maṭbūʿun ʿalā l-taʿabi hayyaʾū lahum aʿyādan li-l-ālihati wa-li-l-sakīnāti wa-li-ʾf-w-l-l-n mudabbiri l-sakīnāti wa-li-d-y-w-n-w-s-y-s māniḥi l-bašari l-ḫamrata dawāʾan lahum min ʿufūṣati l-šayḫūḫati li-yaʿūdū fityānan bi-l-duhūli ʿani l-kābati wa-ntiqāli ḫulqi l-nafsi [wa-yantaqila ḫulqu l-nafsiperhaps to be read] mina l-šiddati ilā l-salāmati [al-salāsatiprobably to be read].

The Athenian said in the second book of the work [sc. theLaws]: The gods, taking pity on the human race since it was born for toil, established for them feast-days (dedicated) to the gods and to the Muses and to Apollo, overseer of the Muses, and to Dionysus, who gave human beings wine as a remedy for them against the bitterness of old age, so that they might be rejuvenated by forgetting sorrow and (by) the character of the soul changing [and (so that) the character of the soul might changeperhaps to be read] from severity into soundness [into tractabilityprobably to be read].

The source of the latter part of the passage, that is, the description of Dionysus’ gift and its effect (māniḥi l-bašari…l-salāmati), has until now remained unidentified. In the notes to his translation, Sachau, followed by Gabrieli, correctly identified part ofLeg. 653c–d (θεοὶ … ἔδοσαν) as the origin of much of the passage (see n. 4). No previous scholarship, however, has noted that the latter part translates a passage inLeg.666b–c (τοῖς ἀνθρώποις … τὸ τῆς ψυχῆς ἦθος), here joined to the earlier passage (presumably by Bīrūnī’s source, that is, most likely Galen) on the hinge of their shared mention of Dionysus.
ΜΕΣΟΤΗΣ IN PLATO'SLAWS746A6–7
Authors: Grasso Roberto
Published: July 2019

In the fifth book of Plato'sLaws(745e7–746a8), the Athenian stranger concedes that some requirements posed in the description of the ideal city might be unrealistically demanding. The passage quotes the due limits fixed with regard to wealth and the regulations about the number of children and the size of the family, as well as the rules to be observed in the allocation of houses in the city and in the countryside. The latter requirement is recalled at 746a6–7 (ἔτι δὲ χώρας τε καὶ ἄστεος, ὡς εἴρηκεν, μεσότητάς τε καὶ ἐν κύκλῳ οἰκήσεις πάντῃ), where the word μεσότης is unanimously understood as indicating a geographic notion of ‘middle’, with regard to either the position of the houses in the ideal city, or that of the city in the territory.
KoszulA∞-algebras and free loop space homology
Authors: Berglund Alexander , Börjeson Kaj
Published: July 2019

We introduce a notion of KoszulA∞-algebra that generalizes Priddy's notion of a Koszul algebra and we use it to construct smallA∞-algebra models for Hochschild cochains. As an application, this yields new techniques for computing free loop space homology algebras of manifolds that are either formal or coformal (over a field or over the integers). We illustrate these techniques in two examples.
Late Cambrian – Early Ordovician magmatism in the Sierra de Pie de Palo, Sierras Pampeanas (Argentina): implications for the early evolution of the proto-Andean margin of Gondwana
Authors: Ramacciotti Carlos D. , Casquet César , Baldo Edgardo G. , Alasino Pablo H. , Galindo Carmen , Dahlquist Juan A.
Published: July 2019

The Sierra de Pie de Palo, in the Argentinean Sierras Pampeanas (Andean foreland), consists of a Mesoproterozoic basement and an Ediacaran – upper Cambrian sedimentary cover that underwent folding, thrusting and metamorphism during the Ordovician Famatinian orogeny. Mafic rocks and granitoids of the easternmost Sierra de Pie de Palo provide information about the magmatic activity at the proto-Andean margin of Gondwana during late Cambrian – Early Ordovician time. Magmatic activity began in the Sierra de Pie de Palo as dykes, sills and small intrusions of tholeiitic gabbros between 490 and 470 Ma, before shortening and regional metamorphism. Variable mantle sources (Nd depleted mantle age, TDM between 1.7 and 1.3 Ga) were involved in the mafic magmatism. Nd-isotope signatures were probably inherited from a Mesoproterozoic subcontinental mantle. Mafic magmatism was coincident with collapse of a Cambrian carbonate-siliciclastic platform that extended along SW Gondwana, and was probably coeval with the beginning of subduction. After mafic magmatism, peraluminous granitoids were emplaced in the Sierra de Pie de Palo along ductile shear zones during a contractional tectonic phase, coeval with moderate to high P/T metamorphism, and with the Cordilleran-type magmatic arc that resulted from a flare-up at c. 470 Ma. Granitoids resulted mainly from partial melting of metasedimentary rocks, although some hybridization with juvenile magmas and/or rocks cannot be ruled out. The evidence shown here further implies that the Pie de Palo block was part of the continental upper plate during the Famatinian subduction, and not an exotic block that collided with the Gondwana margin.
Italian Minor Theatre, 2000–14: the Development of ‘Short Forms’ and the Politics of the Stage
Authors: Mei Silvia
Published: July 2019

Brevity in experimental Italian theatre is not merely an expressive dimension of scenic creation, but a forma mentis, a conceptual vocation of young companies. The 2000s produced a minor theatre in Italy – first because of the reduced stage size, and second because of the brevity of works such as installation pieces. Moving from the linguistic disintegration of the historical avant-gardes of the twentieth century, this theatre is especially inspired by the visual arts, even though its historical roots remain fragmented and art is still seen in the synthetic language of modern dance and Futurist variety. Short forms actually become a tool for crossing artistic genres and languages. Starting from Deleuze’s and Guattari’s philosophical concept of minor literature, in this article Silvia Mei explores and analyzes work by such Italian contemporary companies as gruppo nanou, Città di Ebla, Anagoor, Opera, ErosAntEros, and Teatro Sotterraneo – all representative of what can be called installation theatre, a new theatrical wave that crosses the boundaries and specificities of artistic language, leading to the deterritorialization of theatre itself, a rethinking of the artistic work as well as its relationship with the audience. Silvia Mei is Adjunct Professor of the History of Theatre Directing and Theatre Iconography at the University of Bologna, having been a Research Fellow at the University of Turin. Her recent publications include ‘La terza avanguardia: ortografie dell’ultima scena italiana’, in Culture Teatrali, No. 14 (2015), and Displace Altofest (Valletta: Malta 2018 Foundation).
Neural morphosyntactic tagging for Rusyn
Authors: Scherrer Yves , Rabus Achim
Published: July 2019

The paper presents experiments on part-of-speech and full morphological tagging of the Slavic minority language Rusyn. The proposed approach relies on transfer learning and uses only annotated resources from related Slavic languages, namely Russian, Ukrainian, Slovak, Polish, and Czech. It does not require any annotated Rusyn training data, nor parallel data or bilingual dictionaries involving Rusyn. Compared to earlier work, we improve tagging performance by using a neural network tagger and larger training data from the neighboring Slavic languages. We experiment with various data preprocessing and sampling strategies and evaluate the impact of multitask learning strategies and of pretrained word embeddings. Overall, while genre discrepancies between training and test data have a negative impact, we improve full morphological tagging by 9% absolute micro-averaged F1 as compared to previous research.
Astrobioethics: a brief discussion from the epistemological, religious and societal dimension
Authors: Chon-Torres Octavio A.
Published: July 2019

As astrobiology progresses in its quest to discover life on other planets or to put ourselves in another one, so does its moral problematic. Astrobiology is not only part of natural sciences, but also deals with direct aspects of humanities. For this reason, this paper aims to briefly examine astrobioethics from the epistemological, religious and societal dimension. It also deals with different researches in this regard, in order to better understand the state of the art on this topic and that astrobioethics can help us not only on how we should relate with extraterrestrial lifeforms, but even with terrestrials.
The Cassini Mission May Be Over, but New Discoveries Abound
Authors: Derouin Sarah
Published: July 2019

New analysis of high-resolution images shows ring textures and disruptions within Saturn’s rings in unprecedented detail.
Diurnal Surface Flux Variability Over Western Boundary Currents
Authors: Clayson Carol Anne , Edson James B.
Published: July 2019

An analysis of a satellite ocean surface turbulent flux product demonstrated that, as expected, the western boundary current regions dominate the seasonal cycle amplitude. Surprisingly, our analysis of the global ocean diurnal flux variability also demonstrated a regional maximum in the winter over the western boundary current regions. We conducted comparisons with in situ data from several buoys located in these regions. The buoy data were in general agreement with the relative magnitude, timing, and importance of each of the bulk parameters driving the latent and sensible heat fluxes. Further analysis demonstrated that the strength and timing of the diurnal signal is related to the location of the buoy relative to the region of maximum heat flux and sea surface temperature gradient. In both regions, the timing of the higher winds coincides with the moistest surface layer, indicating that surface fluxes rather than entrainment mixing play a key role in this phenomenon.
Attribution of Detected Temperature Trends in Southeast Brazil
Authors: de Abreu R. C. , Tett S. F. B. , Schurer A. , Rocha H. R.
Published: July 2019

Southeast Brazil has great economic importance for Brazil and is highly vulnerable to extreme events like floods and droughts. Studies have shown an increase of temperature in this region. Using a new detection and attribution framework (Ribes et al., 2017, https://doi.org/10.1007/s00382-016-3079-6) and Coupled Model Intercomparison Project Phase 5 models, this change is found to be largely due to greenhouse gases. We estimate that greenhouse gases contribute a warming of 0.95 to 1.5 °C to the observed warming trend of 1.1 °C between 1955 and 2004. Temperature changes from natural and nongreenhouse gas anthropogenic forcing are estimated to be small over this period. Results are robust using different time windows. Using the Community Earth System Model ensembles to evaluate the impacts of internal variability, observational and model error shows that most uncertainty arises from model error.
Land Cover Regulates the Spatial Variability of Temperature Response to the Direct Radiative Effect of Aerosols
Authors: Chakraborty T. , Lee X.
Published: July 2019

Aerosol impact on the surface temperature varies between the shortwave and the longwave components of radiation, depends on the time of the day, and is modulated by underlying biophysical processes. We disentangle these complexities by isolating the direct surface shortwave and longwave radiative effects from a global reanalysis data product and calculating their spatially explicit climate sensitivities. Higher sensitivity is found for the longwave component and is driven by a combination of spatial variability of aerosol species and biophysical control of the underlying surface. The opposing shortwave and longwave effects reduce the global terrestrial mean diurnal temperature range by 0.47 K, with almost half the contribution in the regions of interest considered coming from aerosols of anthropogenic origin. We also find evidence of an increasing trend in the local climate sensitivity in the equatorial zone, possibly caused by deforestation. These surface processes can partially explain why the climate forcing efficacy of aerosols exceeds unity.
L Versus Time Structures of Dayside Magnetic Pulsations Detected by the European Quasi‐Meridional Magnetometer Array
Authors: Takahashi Kazue , Heilig Balázs
Published: July 2019

We studied the spatiotemporal structure of ground magnetic pulsations on the dayside by displaying magnetic field perturbations detected by the European quasi‐Meridional Magnetometer Array (EMMA) as 2‐D images in the magnetic L value versus time space, called EMMAgrams. We generated EMMAgrams from observations made on 15 August 2015, including a previously studied pulsation event associated with an interplanetary shock. In addition to signatures of field line resonance driven by a cavity mode oscillation, we found poleward propagating structures with L‐independent periods in the Pc2 band. The Pc2 structures are attributed to periodic magnetohydrodynamic pulses (upstream waves) originating from the ion foreshock and propagating in the magnetosphere along the path proposed by Tamao. Ringing of local field lines at L‐dependent periods (transient pulsations) is also clearly detected as dispersive poleward propagating structures not only immediately after the shock impact but also during time periods of less obvious external disturbances. A transient pulsation decays after a few wave periods, and cross‐spectral analysis of transient pulsations detected at two stations with a small latitudinal separation indicates elevation of the cross phase in a band delimited by the field line resonance frequencies at the stations. Successive excitation of transient pulsations by variations of the solar wind dynamic pressure appears to contribute significantly to formation of similar cross‐phase peaks that are widely used in magnetoseismic studies.
New Aspects of the Ionospheric Behavior Over Millstone Hill During the 30‐Day Incoherent Scatter Radar Experiment in October 2002
Authors: Liu Libo , Le Huijun , Chen Yiding , Zhang Ruilong , Wan Weixing , Zhang Shun‐Rong
Published: July 2019

The geomagnetic storm‐driven ionospheric changes and the involved processes are interesting and challenging topics in understanding and predicting the ionosphere. In this study we investigate the response of the ionosphere to geomagnetic disturbances during the 30‐day incoherent scatter radar measurements conducted at Millstone Hill (42.6°N, 71.5°W) from 4 October to 4 November 2002. During geomagnetically disturbed periods, while the peak electron density of the F2 layer (NmF2) and total electron content deviate remarkably from the quiet time ones in a similar way, the incoherent scatter radar measurements reveal that the changes in electron density are frequently different between low and high altitudes. The electron density is significantly depleted at low altitudes; however, at topside it either changes slightly or sometime is enhanced. The enhanced vertical scale height around 600 km under geomagnetically active conditions implies that the topside electron density profiles become much steeper. The increase in the peak height of F2 layer (hmF2) indicates the upward motions under the action of the storm‐driven dynamic processes. Further, sometimes strong differences are shown in total electron content between Millstone Hill and longitude 100°W. The competing contributions from dynamic processes and disturbance composition to the storm‐time ionospheric changes over Millstone Hill are indicated in the different responses in electron density at the bottomside and topside of the ionosphere.
Progression of Parkinson’s disease pathology is reproduced by intragastric administration of rotenone in mice
Authors: Pan-Montojo Francisco , Anichtchik Oleg , Dening Yanina , Knells Lilla , Pursche Stefan , Jung Roland , Jackson Sandra , Gille Gabrielle , Spillantini Maria Grazia , Reichmann Heinz , Funk Richard
Published: July 2019

In Parkinson’s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic blood or the central nervous system (CNS) (detection limit [rotenone]<20nM), indicating that rotenone is detoxified by the liver. These alterations are sequential, appearing only in synaptically connected nervous structures, treatment time-dependent and accompanied by inflammatory signs and motor dysfunctions. These results strongly suggest that the local effect of pesticides on the ENS might be sufficient to induce PD progression and to reproduce the neuroanatomical and neurochemical features of PD staging. Thus, providing new insight into how environmental factors could trigger PD and pointing out a transsynaptic mechanism by which PD might propagate to and through the CNS.
The Evolution of Homochirality
Authors: Wallace Rodrick
Published: July 2019

It is possible to reconsider the origin of biological homochirality in a novel way by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau's spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to 'freeze' the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in a Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process locked in this initial condition, in spite of increases in available metabolic free energy. Astrobiological outcomes, given higher initial metabolic free energy densities, could well be considerably richer, for example, of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemisty, in marked contrast with published predictions of a racemic average.
Metabolic constraints on the evolution of genetic codes: Did multiple 'preaerobic' ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Authors: Wallace Rodrick
Published: July 2019

A mathematical model based on Tlusty's topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the 'aerobic' transition, enabled a punctuated sequence of increasingly complex genetic codes and protein translators under mechanisms similar to the Serial Endosymbiosis effecting the Eukaryotic transition. These evolved until the ancestor to the present narrow spectrum of nearly maximally robust codes became locked-in by path dependence.
Metabolic constraints on the evolution of genetic codes: Did multiple 'preaerobic' ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Authors: Wallace Rodrick
Published: July 2019

A spontaneous symmetry lifting model based on Tlusty's elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low fidelity quasi-equilibria consistent with the 'virus world' hypothesis of Koonin et al. (2006). A more detailed search for empirical evidence of 'preaerobic' ecosystem shifts in metabolic free energy availability or efficiency of use might be surprisingly fruitful.
Using MicroPET Imaging in Quantitative Verification of Acupuncture Effect in Ischemia Stroke Treatment
Authors: Shen Xiaoyan , Tang Hongtu , Li Jia , Xiang Ting , Liu Huafeng , Yu Weichuan
Published: July 2019

While acupuncture has survived several thousand years’ evolution of medical practice, its function still remains as a myth from the view point of modern medicine. Our goal in this paper is to quantitatively understand the function of acupuncture in ischemia stroke treatment. We carried out a comparative study using the Sprague Dawley rat animal model. We induced the focal cerebral ischemia in the rats using the middle cerebral artery occlusion (MCAO) procedure. For each rat from the real acupuncture group (n = 40), sham acupoint treatment group (n = 54), and blank control group (n = 16), we acquired 3-D FDG-microPET images at baseline, after MCAO, and after treatment (i.e., real acupuncture, sham acupoint treatment, or resting according to the group assignment), respectively. After verifying that the injured area is in the right hemisphere of the cerebral cortex in the brain by using magnetic resonance imaging(MRI) and triphenyl tetrazolium cchloride (TTC)-staining, we directly compared the glucose metabolism in the right hemisphere of each rat. We carried out t-test and permutation test on the image data. Both tests demonstrated that acupuncture had a more positive effect than non-acupoint stimulus and blank control (P < 0.025) in increasing the glucose metabolic level in the stroke-injured area in the brain, while there was no statistically significant difference between non-acupoint stimulus and blank control (P>0.15). The immediate positive effect of acupuncture over sham acupoint treatment and blank control is verified using our experiments. The long-term benefit of acupuncture needs to be further studied.
On optical detection of densely labeled synapses in neuropil and mapping connectivity with combinatorially multiplexed fluorescent synaptic markers
Authors: Mishchenko Yuriy
Published: July 2019

We propose a new method for mapping neural connectivity optically, by utilizing Cre/Lox system Brainbow to tag synapses of different neurons with random mixtures of different fluorophores, such as GFP, YFP, etc., and then detecting patterns of fluorophores at different synapses using light microscopy (LM). Such patterns will immediately report the pre- and post-synaptic cells at each synaptic connection, without tracing neural projections from individual synapses to corresponding cell bodies. We simulate fluorescence from a population of densely labeled synapses in a block of hippocampal neuropil, completely reconstructed from electron microscopy data, and show that high-end LM is able to detect such patterns with over 95% accuracy. We conclude, therefore, that with the described approach neural connectivity in macroscopically large neural circuits can be mapped with great accuracy, in scalable manner, using fast optical tools, and straightforward image processing. Relying on an electron microscopy dataset, we also derive and explicitly enumerate the conditions that should be met to allow synaptic connectivity studies with high-resolution optical tools.
ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data
Authors: Khiabanian Hossein , Van Vlierberghe Pieter , Palomero Teresa , Ferrando Adolfo , Rabadan Raul
Published: July 2019

Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants using partially mapped reads in nextgen sequencing data. We also report ParMap’s successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.
Exploitation, secondary extinction and the altered trophic structure of Jamaican coral reefs
Authors: Roopnarine Peter , Hertog Rachel
Published: July 2019

Coral reef communities of the Greater Antilles in the Caribbean have a long history of anthropogenic disturbance, driven by the exploitation for food of both vertebrate and invertebrate species. Exploitation, coupled with region wide declines of coral environments has resulted in local and regional vertebrate extinctions. The impact of those extinctions on reef communities, however, remains largely unexplored. Here we show, using a highly resolved model coral reef-seagrass food web, that at least 40 of 188 expected vertebrate species are absent from Jamaican coral reefs. Twenty one of the absent species are of high trophic level and are exploited by humans. The remainder of the absent species are unexploited, and comprises a significantly high proportion of specialized reef foragers. Many of those species are also more trophically specialized than their closest trophic competitors. We conclude that the absence of unexploited species from Jamaica is caused by the overexploitation of high trophic level species, and consequent trophic cascades and secondary extinction among their prey in an increasingly degraded reef environment. The result is a reef community depauperate of both exploited high trophic level predators, and unexploited, specialized lower trophic level reef foragers.
Homeoprotein Hbx4 represses adhesion molecule governing cytokinesis and development
Authors: Kim Ji-Sun , Seo Ji-Hui , Yim Hyung-Soon , Kang Sa-Ouk
Published: July 2019

Homeobox genes encode proteins with a highly conserved DNA-binding motif and provoke morphological diversification of body segments by differentially controlling the expression of downstream targets. Here, we have identified hbx4, one of many homeobox genes in Dictyostelium discoideum and investigated its role during growth and development. In suspension, Hbx4-overexpressing cells, Hbx4^OE^, showed defects in cytokinesis and growth rate. During development, Hbx4^OE^ and hbx4-disrupting cells, hbx4&175; made differences in shape of mound and slug, cell-type proportioning from wild type KAx3 cells. These phenotypes were similar to those of mutant defective in cadA encoding Ca^2+^-dependent cell adhesion molecule so that we investigated the relationship between hbx4 and cadA. Overexpression of Hbx4 inhibited the expression of cadA and cAMP also failed to stimulate cadA in Hbx4^OE^. Furthermore, gel mobility shift assay showed the promoter of cadA contained Hbx4-binding site, indicating Hbx4 negatively regulates the expression of cadA. Proteome analysis revealed that overexpression of Hbx4 repressed the rdiA and abpB encoding rho guanine nucleotide dissociation inhibitor1, RhoGDI1 and actin bundling protein 34, ABP34, respectively. And the overexpression of cadA in Hbx4^OE^ cells rescued the defects and increased mRNA level of rdiA, abpB and one of Rho GTPase, rac1b. These results suggested that Hbx4 can modulate cytokinesis, cell sorting and cell-type proportioning by repressing cadA that regulates GTPase-dependent signaling pathway.
The response of two legume crops (hyacinth bean and Kidney bean) to the parasitism of field dodder (Cuscuta campestris)
Authors: Farah Awad
Published: July 2019

Abstract: Microscopic examinations and chemical studies were performed to study the response of two legume crops, hyacinth bean (Lablab purpureus L.) Sweet and kidney bean (phaseolus vulgaris L.) to the filed dodder (FD) (Cuscuta campestris Yuncker) parasitism. Hyacinth bean, showing no effective resistance mechanisms,was found to be a highly susceptible host to FD. However, kidney bean, displaying resistant reactions towards the parasitism of FD,was found to be an incompatible host.The possible reasons for the resistance of kidney bean to FD were anatomical (hypersensitivity) and chemical (high contents of phenolic acids and lignin) stimulated defence mechanisms, which developed during the actual intrusion of FD haustorial cells inside its tissues.
Wikipedia as an encyclopaedia of life
Authors: Page Roderic
Published: July 2019

In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision.
Whisker's Directional Selectivity: Orientation Columns in the Barrel Field?
Authors: Tsytsarev Vassiliy , Pope Daniel , Pumbo Elena , Yablonskii Alexander , Hofmann Michael
Published: July 2019

Using voltage-sensitive dye optical imaging methods, we visualized neural activity in the rat barrel cortex in response to the deflection of a single whisker in different directions. Obtained data indicates that fast movements of single whiskers in varying directions correlate with different patterns of activation in the somatosensory cortex. A functional map was created based on the voltage-sensitive dye optical signal. This supports prior research that vibrissae deflections cause responses in different cortical neurons within the barrel field according to the direction of the deflection. By analogy with the orientation columns in the visual cortex, directionally-biased single whisker responses to different directions of deflection could be a possible mechanism for the directional selectivity of this important sensory response.
A Fresh Look at Energy, Materials, and Labor in Agriculture
Authors: Baum Aaron , Patzek Tadeusz , Bender Martin , Renich Steve , Jackson Wes
Published: July 2019

An understanding of agriculture's energy, material, and labor requirements is essential for achieving economic and ecological sustainability, and for assessing the effectiveness of relevant policy decisions (biofuel subsidies, regulations, labeling, etc.). Previous studies of energy, materials, and labor use in farming have been based on either unverified voluntary reporting or test plots, rather than on the high-resolution measurements of mass and energy flows. Here we present a recursive analysis of 1.25 million data points describing in unprecedented detail the resource transactions on a 60 ha farm functioning for over 6 years. This analysis highlights the importance of accounting for all types of materials, as well as capital equipment, non-field labor, and commuting. The superior energy efficiency of the farm's energy-saving methods, including green manure, crop rotation, composting, and short-duration grazing -- compared with conventional methods -- persists even when the higher labor requirements are taken into account. One of the farm's methods, however -- the use of horses for traction -- is shown to be highly inefficient compared with mechanical tractors.
A Roadmap of Cancer Systems Biology
Authors: Wang Edwin
Published: July 2019

What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed.
Processing of insect retrotransposons by self-cleaving ribozymes
Authors: Ruminski Dana , Webb Chiu-Ho , Riccitelli Nathan , Luptak Andrej
Published: July 2019

We show that several classes of insect non-LTR retrotransposons harbor self-cleaving ribozymes of the HDV family at their 5′ termini. In Drosophila the R2 ribozymes exhibit highly differential in vivo expression and robust in vitro activity, modulated by an upstream sequence originating from the insertion site. Our data suggest a role for self-cleaving ribozymes in co-transcriptional processing of retrotransposons with implications for downstream events, including translation and retrotransposition.
Protein folding disorders: Toward a basic biological paradigm
Authors: Wallace Rodrick
Published: July 2019

Mechanistic 'physics' models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tumor suppressors p53, p63, and p73 inhibit migrating cancer stem cells by increasing the expression of stem cell suppressing miRNAs
Authors: Boominathan Lakshmanane
Published: July 2019

ZEB1/2 has been shown to suppress the expression of the tumor suppressors E-cadherin, TA-p73, INK4b, CDKN1a, and thereby promotes epithelial to mesenchymal transition, invasion, and metastasis. I have recently shown that p53-dependent miRs, such as miR-192, 215, 145, 203, 200b/c, 183, suppress the expression of ZEB1/2. Another recent study showed that ZEB1/2 suppresses the expression of miR-200b/c, miR-203, & miR-183, which in turn, inhibit the expression of stem cell factors, such as Sox-2, Klf-4, and BMI. ZEB1/2, by inhibiting the expression of stem cell factors suppressing miRs, it up regulates the expression of stem cell factors. By up regulating the stem cell factors and down regulating metastasis suppressors, ZEB1/2 promotes both metastasis and migration of cancer stem cells. p53/p63/p73, by down regulating the expression of ZEB1/2 through its target miRNAs, it could activate the expression of stem cell suppressing miRNAs, such as miR-200b/c, miR-203 & miR-183. Thereby, it could inhibit the expression of stem cell factors, such as Sox-2, Klf-4 and BMI-1(an inhibitor of INK4a/ARF). In addition, p53/p63/p73 appears to inhibit the expression of other EMT inducers, such as Snail1/2 and Twist, expression through its target miRs. Remarkably, bioinformatics analysis of stem cell factors suppressing miRNAs, miR-200, miR-183, miR-141, and miR-203, promoters revealed a number of p53/p63/p73 responsive elements, indicating that they could be direct transcriptional targets of p53/TA-p63/p73. Together, these data suggest that p53/TA-p63/p73, by suppressing the expression of ZEB1/2, Snail1/2, and Twist through its target miRs, it could inhibit migration, metastasis, and proliferation of cancer stem cells. In conclusion, the data presented here provide mechanistic insights into how TA-p63/p73 and p53 function as metastasis suppressors.
The last Charrua Indian; (Uruguay): analysis of the remains of Chief Vaimaca Per&x00FA;.
Authors: Sans Monica , Figueiro Gonzalo , Sanguinetti Carlos , Echarte-Rafaelli Lourdes , Portela Cecilia , Taranto Luis , Pizzarossa Carlos , Oliver Roberto , Manikowski Rosana , Barreto Isabel , Hidalgo Pedro , Berro Guido
Published: July 2019

Uruguay is the only Latin American country that at present lacks Native populations and little is known about its prehistoric populations. In the construction of National identity, the unique reference to Natives is about Charra Indians, one of the most important ethnic groups that lived in the territory and exterminated in the 1830s. In 1833, four survivors were taken to be exhibited and studied in France, becoming martyrs and a symbol of their nation. The skeletal remains of Chief Per&x00FA; were preserved and studied mainly by Rivet1; these are the only remains certainly identified as belonging to a Charr&x00FA;a. In 2002, the French government returned the remains to Uruguay, where they were buried with honours at the National Pantheon. Before the burial, we performed morphological studies as well as extracted samples for DNA analysis. Peru's morphology is coherent with the one of a nomadic warrior: robust body with strong muscular insertions, wounds, and healthy diet based mainly on meat. Here we show that metric and morphological data as well as maternal inherited mitochondrial DNA (mtDNA) hypervariable region I (HVRI) and restriction fragment length polymorphisms (RFLPs), indicate a close relationship with Pampa-Patagonian Indians, and specially, with prehistoric Natives buried in mounds from eastern Uruguay. This last finding is particularly important to understand Uruguayan prehistory and history, raising the debate about who the mound builders were, and showing continuity between them, historic Charr&x00FA;a Indians, and present populations.