bluuebunny/crossref_metadata_2025 huggingface dataset:
Fruit set in a deceptive orchid: The effect of flowering phenology, display size, and local floral abundance
Authors: Sabat Alberto M. , Ackerman James D.
Published: January 2018

We investigated the effect of flowering time, display size, and local floral density on fruit set in Tolumnia variegata, a pollination‐limited orchid that offers no reward to its pollinator(s). During 1990, natural variation in flowering time, display size, and fruit set were monitored in 508 plants at one locality in Puerto Rico. The following season, orchid floral abundance per host tree (Randia aculeata) was manipulated to investigate its effect on fruit set. Four floral abundance treatments were established (700, 500, 300, and 100), each replicated four times. Flowering time was the most important trait affecting fruit set. The proportion of plants setting at least one fruit was significantly high early and late in the season, but low during the flowering peak. Thus, strong disruptive selection differential on flowering phenology was found. Display size had little effect on fruit set. A weak, but significant disruptive selection differential on display size was found. Orchid floral abundance per host tree had a significant effect on fruit set. Early in the season, T. variegata flowers with intermediate number of conspecific flowers exhibited a greater probability of setting fruit than those in host trees with fewer or more flowers. Our results show that flowering phenology may be evolutionarily unstable, possibly a consequence of the deception pollination system. Furthermore, a deception strategy would be relatively unsuccessful in populations where plants are found in either very dense or sparse patches.
Phylogeny of Agavaceae based on ITS rDNA sequence variation
Authors: Bogler David J. , Simpson Beryl B.
Published: January 2018

Several systems of classification have been proposed for the family Agavaceae. A distinctive bimodal karyotype and similarities of fruits and seeds strongly support close relationships among Yucca, Hesperaloë, Beschorneria, Furcraea, Agave, Manfreda, Polianthes, Prochnyanthes, and perhaps Hosta. However, Dasylirion, Beaucamea, Nolina, Calibanus, Dracaena, and Sansevieria differ in so many cytological and morphological features that many have concluded they should be excluded from Agavaceae and separated into two families, Nolinaceae and Dracaenaceae. Chloroplast DNA restriction site data support these separations and indicate that Nolinaceae and Dracaenaceae are very close to Convallariaceae (Maianthemum, Convallaria, Aspidistra, Liriope, etc.). In this paper we report the results of an ITS rDNA sequencing study of 40 taxa in Agavaceae sensu lato and related groups in the order Asparagales. Sequence alignments were optimized using the Consistency Index, Retention Index, and Rescaled Consistency Index to find the alignment that exhibited the least amount of homoplasy. The results of our study are congruent with the conclusions drawn from cytological, immunological, cpDNA, and rbcL studies, which support a narrow interpretation of Agavaceae and a close relationship among Convallariaceae, Dracaenaceae, and Nolinaceae. In addition, the ITS sequence data provide evidence for some interesting relationships within these families.
Exsertion, flowering, and shedding in Panicum maxicum (Poaceae)
Authors: Noirot Michel , Ollitrault Patrick
Published: January 2018

Within‐panicle flowering, exsertion, and seed ripening were investigated in four clones of P. maximum. Flowering, exsertion, and seed ripening were fast processes (<;10 d for each process). Dates and timing were stable within each clone and should allow definition of the harvest date for each genotype and for each harvest method. Clones showed two main flowering patterns differing in the number of flowered spikelets at the date of maximal flowering and in the time of flowering. Seed set was similar to that of allogamous and anemophilous plants. It was nevertheless lower in clones with a high degree of flowering‐shedding overlap. In the absence of flowering‐shedding overlap, the time for a panicle to flower and to produce seeds was shorter than the time between two emergences of panicles on a tiller. Reproduction timing seemed controlled to minimize competition between panicles on a tiller.
Molecular divergence between disjunct taxa in eastern Asia and eastern North America
Authors: Lee Nam Sook , Sang Tao , Crawford Daniel J. , Yeau Sung Hee , Kim Seung‐Chul
Published: January 2018

Eastern Asian‐eastern North American disjuncts in four genera were examined for allozyme divergence and sequence divergence of the internal transcribed spacers (ITS) of nuclear ribosomal DNA. The disjunct pairs of taxa include Caulophyllum robustum‐C. thalictroid.es, Menispermum dauricum‐M. canadense, Penthorum chinense‐P. sedoides, and Phryma leptostachya var. asiatica‐P. leptostachya var. leptostachya. Allozyme divergence was comparable in Caulophyllum and Penthorum (genetic identities of 0.534 and 0.546) and was considerably higher than between pairs of taxa in Menispermum (0.273) and Phryma (0.291). Caulophyllum and Penthorum, which have the highest genetic identities at allozyme loci, also have low ITS sequence divergences (1.30 and 1.65%, respectively). Phryma, which has low isozyme identity, also has the highest ITS sequence divergence (4.46%). The two taxa of Menispermum have low ITS sequence divergence (0.93%) despite having a low identity (0.273) at allozyme loci. The results suggest that divergence between the taxa in the four genera are not the result of a single historical event. Estimated divergence times are reasonably consistent with a late Miocene disjunction for Caulophyllum and Penthorum, whereas the age of the Phryma disjunction is calculated at over 20 million years. The nonconcordant divergences between allozymes and ITS sequences in Menispermum may be caused by concerted evolution in the latter or possibly longer generation time in the woody plants. Additional molecular data are needed to clarify the situation.
Population density and module demography in Trapa natans (Trapaceae), an annual, clonal aquatic macrophyte
Authors: Groth Anne T. , Lovett‐Doust Lesley , Lovett‐Doust Jon
Published: January 2018

The effects of population density on module demography were studied in Trapa natans L., an annual aquatic macrophyte capable of extensive clonal propagation. At low density, the floating plants produced ten times as many ramets (clonal offshoots) as those at high density. Module mortality occurred at three levels: leaf, ramet (shoot), and genet (genetic individual). There was 100‐fold variation in the size of nuts containing germinable seeds. In early summer there was a highly significant linear relationship between dry mass of nuts and the total mass of ramets that each had produced. In early summer most (73–83%) of the variation in total plant biomass was attributable to variation in initial nut size. However the significance of initial nut size was diminished later in the season. The great success of the exotic weed T. natans at colonizing and monopolizing an aquatic habitat is a function of its highly productive clonal growth response to low‐density conditions, combined with greater proportional allocation of biomass to reproductive structures, resulting in greatly increased nut production at low initial density. The species appears able to develop and maintain a population at extremely high density: plant buoyancy and the production of large, well‐protected nuts allow rapid early growth from the sediment each year and early pre‐emption of the water surface.
Parallelism and diversity in multiple origins of c4 photosynthesis in the grass family
Authors: Sinha Neelima R. , Kellogg Elizabeth A.
Published: January 2018

C4 photosynthesis is thought to be an adaptation to warm environments, involving complex changes in the expression of genes governing photosynthesis, intermediary metabolism, and leaf anatomy and histology. Such complexity should be difficult to evolve, yet the pathway has arisen multiple times in the history of the flowering plants and at least four times in the grass family alone. We have used immunolocalization techniques to compare photosynthetic gene expression across all four origins, to determine which genetic changes occur in parallel and which are unique to a particular lineage. The only gene expression patterns common to all origins of the pathway are up‐regulation of PEP carboxylase and down‐regulation of RuBisCO in mesophyll cells. Both NAD‐malic enzyme and NADP‐malic enzyme are expressed in bundle sheaths. Expression patterns of light‐harvesting chlorophyll a/b binding proteins and pyruvate orthophosphate dikinase appear to be lineage specific, and may be localized to bundle sheaths or to mesophyll or expressed throughout the photosynthetic tissue of the leaf. We suggest that future studies of parallel origin of the C4 pathway concentrate on regulation of the two carboxylases, as well as the increased density of vascular tissue, which is the only histological characteristic common to all origins of the pathway.
Developmental morphology of female flowers of Gyrostemon and Tersonia and floral evolution among Gyrostemonaceae
Authors: Hufford Larry
Published: January 2018

Floral simplifications and specializations in the evolution of Gyrostemonaceae have confused the systematics of the family. Recent phylogenetic analyses have demonstrated their placement among Capparales. This investigation presents a phylogenetic analysis of Gyrostemonaceae, demonstrating that Codonocarpus and Gyrostemon form a clade that is the sister group of Cypselocarpus, Tersonia, and Walteranthus. These phylogenetic results and data on development of Gyrostemon and Tersonia are used to discuss the morphology and evolutionary diversification of female flowers of Gyrostemonaceae. The uniseriate perianth of Gyrostemonaceae consists of four to eight tepals with an unusual lateral to median developmental sequence. The female flowers of Gyrostemon and Tersonia display no distinctive evidence of an androecium, although the former has late‐forming, primordium‐like structures positioned between the tepals and gynoecium that may be the vestiges of either a second perianth series or the androecium. The gynoecium of Gyrostemonaceae is syncarpous, although the two main clades in the family differ in the expression of ovarian synorganization. The Codonocarpus–Gyrostemon clade is unusual in having largely separate carpels that are only syncarpous because the ventral side of each is formed by the flank of the floral apex. All Gyrostemonaceae, however, incorporate the flank of the floral apex as the ventral side of the carpel, and this is the location of ovule development. On the basis of its placement in a clade that includes Tersonia and Walteranthus, the uniloculate and uniovulate gynoecium of Cypselocarpus may be pseudomonomerous. All Gyrostemonaceae have large stigmas that are typical of anemophilous taxa, and they differ from most other Capparales in this attribute. Among Capparales, Gyrostemonaceae may be most similar to Ochradenus (Resedaceae), which also appears to be anemophilous. It is unclear whether the similarities of Ochradenus and Gyrostemonaceae are homologies, indicative of a close relationship between the two groups, or evolutionary parallelisms associated with separate shifts to anemophily.
When Good Things Feel Closer and Bad Things Feel Farther: The Role of Perceived Control on Psychological Distance Perception
Authors: Han Jerry J. , Gershoff Andrew D.
Published: January 2018

Prior research has found that people perceive positive objects and locations as physically closer than negative ones. Yet, other work has found the opposite to be true for perceptions of temporal distance, where negative future events feel closer than positive ones. Motivated by this seeming discrepancy, we propose that (a) feelings of control can differentially influence how far away valenced (i.e., positive or negative) targets feel in space and time and that (b) the difference in perceived control over space versus time can account for these opposite findings. First, across four studies, we show that high (vs. low) control makes positive targets feel closer and negative targets feel more distant in both physical space (Studies 1 and 1a) and time (Studies 2 and 2a). Then, in Studies 3 and 4, we simultaneously examine perceptions of spatial and temporal distance and show that baseline differences in perceived control between these domains can explain the prior discrepant findings. Finally, a within‐paper meta‐analysis offers further support to these findings.
Generalized boosted modeling to identify subgroups where effect of dabigatran versus warfarin may differ: An observational cohort study of patients with atrial fibrillation
Authors: Wang Shirley V. , Huybrechts Krista F. , Fischer Michael A. , Franklin Jessica M. , Glynn Robert J. , Schneeweiss Sebastian , Gagne Joshua J.
Published: January 2018

Purpose

To explore generalized boosted modeling (GBM) as a method for identifying subgroups with greater benefit or harm with dabigatran versus warfarin for treatment of atrial fibrillation.

Methods

We identified new initiators of warfarin or dabigatran with nonvalvular atrial fibrillation in 2 healthcare claims databases (2009–2013) and used GBM within 1 data source (development cohort) to explore subgroups where their effect on thromboembolism and major bleeding may differ. Identified subgroups were evaluated in the second data source (validation cohort) with stabilized‐inverse‐probability‐of‐treatment weights to adjust for confounding.

Results

Development and validation cohorts included 13 624 (28% dabigatran) and 62 596 (29% dabigatran) initiators, respectively. In development data, the strongest exposure interactions were prior thromboembolism and renal disease. In validation data, reduction in thromboembolism with dabigatran was greater for patients with versus without a history of thromboembolism by 2.8 (95% CI, −0.5 to 5.4) events per 100 patient‐years. Major bleeding was reduced by 1.6/100 patient‐years for dabigatran compared to warfarin initiators, without evidence of variation by renal disease.

Conclusions

We explored use of GBM to identify potential subgroups with different treatment effect. Dabigatran's superiority to warfarin at prevention of thromboembolism may be greater in secondary than primary prevention. In practice, secondary prevention patients are more often treated with warfarin.
Label‐Free Quantitative Proteomic Screening of Candidate Plasma Biomarkers for the Prognosis of Breast Cancer with Different Lymph Node Statuses
Authors: Chen Ling , Zhao Weibo , He Jing , Li Liqi , Meng Dong , Cai Dongyan , Yu Jinjin , Chen Daozhen , Wu Yibo , Zhou Tao
Published: January 2018

Purpose

Lymph node status is a crucial predictor for the overall survival of invasive breast cancer. However, lymph node involvement is only detected in about half of HER2‐positive patients. Since patients with lymph node involvement has less favorable prognosis and higher risk of recurrence, it is important to develop plasma protein biomarkers for distinguishing lymph node metastasis.

Experimental design

A label‐free quantitative proteomic strategy to construct plasma proteomes of ten patients with small size HER2‐positive breast cancer (five patients with lymph node metastasis versus five patients without lymph node metastasis) is applied.

Results

A total of 388 proteins are identified, of which 33 proteins are differentially expressed. Statistical analyses suggested the present strategy is low cost and highly efficient in initial screening of plasma biomarkers. In silico analyses using various bioinformatics databases show that these altered proteins are highly associated with breast disease, cancer pathway, lymph node morphology, metastasis, complement pathway, and immune regulation.

Conclusions and clinical relevance

The present dataset provides a list of candidate biomarkers that could be used for early differentiation diagnosis and prognosis of breast cancer with lymph node metastasis.
Minimization of Optical Reflectance by Copper Assisted Etching of Crystalline Silicon Surface
Authors: Treideris Marius , Rėza Alfonsas , Kamarauskas Mindaugas , Mironas Audružis , Strazdienė Viktorija , Maneikis Andrius , Bukauskas Virginijus , Šetkus Arūnas
Published: January 2018

Reduction of the optical reflectance to an absolute minimum by the metal‐assisted chemical etching (MACE) is investigated for the p‐type crystalline silicon (100) plane wafers. The amount of the Cu additive and the composition of the etching solution identified by the proportion HF/(HF + H2O2) are the main variable parameters controlling the one step MACE. Pyramid like structures are produced on the surfaces. An influence of the variables on the surface topography and the related optical reflectance spectra is studied by measuring the spectra in the interval of the wavelengths from 400 to 1400 nm. Presence of a minimum that limits a reduction of the optical reflectance by the maskless micro‐texturing of a smooth surface of a silicon wafer is experimentally demonstrated. The crucial stage in the etching is identified by the relative depth of the etched dips that results in the lowest reflectance. Under strictly controlled conditions the minimum reflectance is obtained using etchant with 0.08 M Cu‐added. The lower and higher amounts of added Cu lead to an increase in the reflectance. The etching is explained by the localized microscopic galvanic cell model including the formation of the Cu‐nanoparticles during the MACE and the changes in the reflectance are related to an enlargement of the etched pyramids.
Luminescent Properties and Optical Amplification of Erbium‐Doped Nano‐Engineered Scandium‐Phospho‐Yttria‐Alumina‐Silica Glass Based Optical Fiber
Authors: Reddy Pinninty Harshavardhan , Das Shyamal , Dutta Debjit , Dhar Anirban , Kir'yanov Alexander V. , Pal Mrinmay , Bhadra Shyamal Kumar , Paul Mukul Chandra
Published: January 2018

In this work, a new erbium (Er) doped nano‐engineered scandium‐phospho‐yttria‐alumina‐silica (SPYAS) glass‐based optical fiber is reported, fabricated through the MCVD process, and solution doping technique, followed by a suitable thermal annealing of pristine preform. The fabrication process comprises the incorporation of erbium doped phase‐separated scandium‐yttria rich crystalline nanoparticles into the core region through in situ process based on phase‐separation and crystal growth phenomena. The material characterization results, obtained from transmission electron microscopy, electron diffraction pattern, energy dispersive X‐ray, electron probe micro analysis, and X‐ray fluorescence, confirm the formation of Er2O3 doped crystalline phase‐separated scandium‐yttria rich nanoparticles in the core region. The formation of scandium‐ultra rich nano‐crystalline environment, possessing low photon energy around the erbium ions, enhanced the fluorescence intensity. Such kind of nano‐engineered glass reduces the noise figure around 4.35 dB, and provides broadband optical flat gain with an average value of 38.675 dB, varied by less than ±0. 7 dB spanning over a broad wavelength region of 1530–1590 nm compared to the pristine and Sc free Er‐doped fibers. Such kind of nano‐engineered glass based Er doped fiber will be useful for making highly efficient optical amplifiers, suitable for present broadband optical communication systems.
Constructing 2D/2D Fe2O3/g‐C3N4 Direct Z‐Scheme Photocatalysts with Enhanced H2 Generation Performance
Authors: Xu Quanlong , Zhu Bicheng , Jiang Chuanjia , Cheng Bei , Yu Jiaguo
Published: January 2018

Sunlight‐driven photocatalytic water splitting to generate hydrogen (H2) is a promising approach for utilizing solar energy. Herein, direct Z‐scheme Fe2O3/g‐C3N4 photocatalysts are rationally fabricated for H2 evolution under visible light. The graphitic carbon nitride (g‐C3N4) nanosheets obtained by solvent exfoliation of bulk g‐C3N4 display modest photocatalytic activity. Strikingly, its photocatalytic performance can be greatly improved by electrostatically assembling with hematite α‐Fe2O3 nanoplates. With platinum (Pt) as co‐catalyst and triethanolamine (TEOA) as hole scavenger, the H2 generation rate of optimized Fe2O3/g‐C3N4 composite with Fe2O3 weight percentage of 10% is about 13‐fold that of g‐C3N4. Based on the enhanced photocatalytic performance and slower time‐resolved photoluminescence decay, Z‐scheme charge transfer process is accepted for running this photocatalytic system, which is further evidenced by selective photo‐deposition of Pt nanoparticles on the g‐C3N4 surface. This rationally synthesized Fe2O3/g‐C3N4 composite is expected to have great potentials in solar energy conversation.
Synthesis of Novel Amino Lactose and Evaluation of Its Antioxidant Property
Authors: Li Qing , Feng Yan , Gu Guodong , Guo Zhanyong
Published: January 2018

In order to improve the bioactivity of lactose, a novel lactose derivative is designed and synthesized by introducing an amino group to the C‐6 of lactose. The in vitro antioxidant activities of synthesized lactose derivatives are assessed. It shows better scavenging activity against hydrogen peroxide (IC50 < 0.1 mg mL−1), hydroxyl radicals (IC50 0.55 mg mL−1), and DPPH radicals (IC50 0.37 mg mL−1) than lactose. Based on this data, it is reasonable to propose that the introduction of amino group through chemical modification is significant to enhance the free antioxidant activity of lactose. This derivatization strategy might provide an effective tool to broaden utilization of lactose.
Global-Mode Analysis of Full-Disk Data from the Michelson Doppler Imager and the Helioseismic and Magnetic Imager
Authors: Larson Timothy P. , Schou Jesper
Published: January 2018

Building upon our previous work, in which we analyzed smoothed and subsampled velocity data from the Michelson Doppler Imager (MDI), we extend our analysis to unsmoothed, full-resolution MDI data. We also present results from the Helioseismic and Magnetic Imager (HMI), in both full resolution and processed to be a proxy for the low-resolution MDI data. We find that the systematic errors that we saw previously, namely peaks in both the high-latitude rotation rate and the normalized residuals of odd $a$
a
-coefficients, are almost entirely absent in the two full-resolution analyses. Furthermore, we find that both systematic errors seem to depend almost entirely on how the input images are apodized, rather than on resolution or smoothing. Using the full-resolution HMI data, we confirm our previous findings regarding the effect of using asymmetric profiles on mode parameters, and also find that they occasionally result in more stable fits. We also confirm our previous findings regarding discrepancies between 360-day and 72-day analyses. We further investigate a six-month period previously seen in $f$
f
-mode frequency shifts using the low-resolution datasets, this time accounting for solar-cycle dependence using magnetic-field data. Both HMI and MDI saw prominent six-month signals in the frequency shifts, but we were surprised to discover that the strongest signal at that frequency occurred in the mode coverage for the low-resolution proxy. Finally, a comparison of mode parameters from HMI and MDI shows that the frequencies and $a$
a
-coefficients agree closely, encouraging the concatenation of the two datasets.
FROM OVERT TO VEILED SEGREGATION: ISRAEL'S PALESTINIAN ARAB CITIZENS IN THE GALILEE
Authors: Shafir Gershon
Published: January 2018

This article's geographical focus is the Galilee, Israel's only region with a Palestinian Arab majority. Its sociological focus is the drive to Judaize this region, the mirror image of its de-Arabization, which I anchor in Israelis’ morbid fear of settler colonial reversal. Although direct legal discrimination—restriction of movement under a military government and exclusion from publicly administered land—was banned by the government and the High Court of Justice respectively, new modes of discrimination against Israel's Arab citizens have replaced the older forms. I demonstrate how policies that limit Arab middle-class citizens’ upwardly mobile migration into the Judaized spaces of communal settlements (or overlooks) and towns endure. I compare gatekeeping exercised by national-level indirect legal discrimination operating through the admission committees of communal settlements with the institutional discrimination practiced by municipalities of emerging mixed towns against new Arab residents’ public presence. Finally, I highlight the linkages between instances of Judaization across the Green Line, which make the unwinding of segregation, in all of its forms, that much harder.
THE MISSING TURKISH REVOLUTION: COMPARING VILLAGE-LEVEL CHANGE AND CONTINUITY IN REPUBLICAN TURKEY AND SOVIET CENTRAL ASIA, 1920–50
Authors: Tuna Mustafa
Published: January 2018

The Kemalist leadership of early Republican Turkey attempted to transform the country's Muslim populace with a heavy emphasis on secularism, scientific rationalism, and nationalism. Several studies have examined the effects of this effort, or the “Turkish Revolution,” at the central and more recently provincial levels. This article uses first-hand accounts and statistical data to carry the analysis to the village level. It argues that the Kemalist reforms failed to reach rural Turkey, where more than 80 percent of the population lived. A comparison with sedentary Soviet Central Asia's rural transformation in the same period reveals ideology and the availability of resources as the underlying causes of this failure. Informed by a Marxist–Leninist emphasis on the necessity of transforming the “substructure” for revolutionary change, the Soviet state undermined existing authority structures in Central Asia's villages to facilitate the introduction of communist ideals among their Muslim inhabitants. Turkey's Kemalist leadership, on the other hand, preserved existing authority structures in villages and attempted to change culture first. However, they lacked and could not create the resources to implement this change.
POINT OF NO RETURN? PROSPECTS OF EMPIRE AFTER THE OTTOMAN DEFEAT IN THE BALKAN WARS (1912–13)
Authors: Öztan Ramazan Hakkı
Published: January 2018

In late 1912, the Ottoman imperial armies suffered a series of quick defeats at the hands of the Balkan League, comprising Greece, Serbia, Bulgaria, and Montenegro, resulting in significant territorial losses. The Ottoman defeat in the Balkan Wars (1912–13) often stands at the center of teleological accounts of a neat and linear transition from Ottoman Empire to Turkish Republic. These teleological readings see the Ottoman defeat as a historical turning point when Ottoman elites turned nationalist, discovered Anatolia, and embraced the Turkish core. This article contends that such approaches frame late Ottoman history in anticipation of the later reality of nation-states, and overlook the messy and historically complex nature of the collapse of empire and the emergence of the nation-state. Although the defeat was certainly shocking for the Ottoman ruling elite, I argue that it initiated an era of debate rather than one of broad consensus. Similarly, the defeat neither marked the end of the Ottoman Empire nor heralded the coming of the Turkish Republic, but rather reinvigorated the Ottoman imperialist project.
Digitizing the Textual Heritage of the Premodern Islamicate World: Principles and Plans
Authors: Miller Matthew Thomas , Romanov Maxim G. , Savant Sarah Bowen
Published: January 2018

The varied textual traditions of the premodern Islamicate World represent an opportunity and a problem for the Digital Humanities (DH). The opportunity lies in the sheer extent of this textual heritage: if we combine the textual output of premodern Persian and Arabic authors (not to mention Turkish and other less well-represented Islamicate languages), this body of texts constitutes arguably the largest written repository of human culture. Analytical methods developed for other linguistic heritages can be repurposed to make use of this wealth of texts, and efforts are now underway to apply to them a series of computationally enhanced methods that derive from a variety of disciplines (e.g., corpus linguistics, computational linguistics, the social sciences, and statistics). The application of these forms of analysis to these large new corpora promises new insights on premodern Islamicate cultures and the improvement of existing digital tools and methodologies.
A RESPONSE TO BRUCE MASTERS’ REVIEW OF MUSLIM–CHRISTIAN RELATIONS IN LATE OTTOMAN PALESTINE: WHERE NATIONALISM AND RELIGION INTERSECT (IJMES 49 [2017]: 191–93)
Authors: Freas Erik E.
Published: January 2018

The following is written with a dual purpose: to respond to Bruce Masters’ review of my recently published monograph, Muslim-Christian Relations in Late-Ottoman Palestine; but more importantly, to suggest that it might be time that Middle East historians reevaluate the manner of our assessment of the value and proper use of “Western” (i.e., nonindigenous) sources in researching and writing about the region's history.
Singular perturbations in noisy dynamical systems
Authors: MATKOWSKY B. J.
Published: January 2018

Consider a deterministic dynamical system in a domain containing a stable equilibrium, e.g., a particle in a potential well. The particle, independent of initial conditions, eventually reaches the bottom of the well. If however, the particle is subjected to white noise, due, e.g., to collisions with a population of smaller, lighter particles comprising the medium through which the particle travels, a dramatic difference in the behaviour of the Brownian particle occurs. The particle will exit the well. The natural questions then are how long will it take for it to exit and from where on the boundary of the domain of attraction of the deterministic equilibrium (the rim of the well) will it exit. We compute the mean first passage time to the boundary and the mean probabilities of the exit positions. When the noise is small each quantity satisfies a singularly perturbed deterministic boundary value problem. We treat the problem by the method of matched asymptotic expansions (MAE) and generalizations thereof. MAE has been used successfully to solve problems in many applications. However, there exist problems for which MAE does not suffice. Among these are problems exhibiting boundary layer resonance, i.e., the problem of ‘spurious solutions’, which led some to conclude that this was ‘the failure of MAE’. We present a physical argument and four mathematical arguments to modify or augment MAE to make it successful. Finally, we discuss applications of the theory.
THE RISE OF THE CHINGGISID DYNASTY: PRE-MODERN EURASIAN POLITICAL ORDER AND CULTURE AT A GLANCE
Authors: Munkh-Erdene Lhamsuren
Published: January 2018

Analyzing the messages and the responses that Chinggis Khan sent to and received from Ong Khan and his allies after his defeat at the hands of the latter at the battle of Qalaqaljit Elet in the spring of 1203, and explicating the terms of cimar (chimar) and törü that appear in the messages, this article looks at the political order and culture where the Chinggisid state rose. The article argues that pre-modern Mongolian and Inner Asian politics was guided by the idea of törü, which resembles the Indo-Buddhist idea of dharma, the Chinese idea of dao, and the European idea of natural law. It also argues that the hereditary divisional system that the Inner Asian state builders regularly employed to govern their nomadic populations, the institutions of dynastic succession, and the hereditary rights of princes and the nobility for inheritance fundamentally structured Inner Asian politics. Hence, it questions the conventional wisdom that depicts pre-modern Inner Asian politics not only as pragmatic, fluid, and fractious but also dependent on the personal charisma of leadership, and the personal bond and loyalty between leaders and followers, as if it were lacking enduring social, political institutions and order.
Probing the Heart and Mind of the Viewer: Scientific Studies of Film and Theater Spectators in the Soviet Union, 1917–1936
Authors: Toropova Anna
Published: January 2018

A vast array of research institutes and cultural organizations began to study the viewer of Soviet cinema and theatre in the years following the October Revolution. These investigations called on the techniques of sociology, psychology, and physiology to make Soviet cultural production more “efficient” and “rational.” Belying the conventional assumption that the cultural revolution of 1928–1932 brought empirical research in aesthetics to an abrupt end, this paper traces the continuation and redefinition of studies of the viewer in the Soviet Union after the “Great Break.” My analysis of the work of the “Scientific Research Sector” at the State Institute of Cinematography (VGIK) between 1933 and 1936 outlines how Stalin-era researchers shifted their gaze from viewers’ tastes and attitudes to questions of perceptual management and effectiveness. Exploring the VGIK researchers’ attempts to determine the “laws” of aesthetic perception and optimize intelligibility, the article brings to light the developments in scientific knowledge underwriting Soviet culture's transition to a form “accessible to the millions.”
Between Scholarship and Dissidence: The Dissident Historical CollectionPamiat΄ (1975–1982)
Authors: Martin Barbara , Sveshnikov Anton
Published: January 2018

This article examines the history of the Soviet dissident historical collectionPamiat΄through the lens of liminality. It argues that the publication sought to bridge the gap between dissident and professional scholarship, between grassroots memory collection, with its emphasis on the witness's voice, and historical research's reliability and “scientificity.” AlthoughPamiat΄was inspired by earlier dissident historiographical projects and its editorial team was closely linked to the human-rights movement, its ambitions of objectivity and representativeness also connect it to later Perestroika projects based on citizen involvement, such asMemorial.Pamiat΄s ambiguous identity and claim to neutrality may have delayed the Soviet authorities’ response to it, but repression eventually hit the publication. By putting into question the state's monopoly on historical scholarship and connecting readers and contributors across the Iron Curtain,Pamiat΄had clearly overstepped the boundaries of the permissible and acquired a political meaning it disingenuously claimed not to have.
Confessing to Leviathan: The Mass Practice of Writing Autobiographies in the USSR
Authors: Zaretskiy Yury
Published: January 2018

Yury Zaretskiy's article examines the mass practice of composing formal autobiographies by Soviet citizens. The major part of the study covers the period from the 1950s to the 1980s when the Soviet records management protocol requested this type of document from individuals belonging to different social groups and to different occupations. Zaretskiy reviews the concrete social circumstances in which the narrative structure of formal autobiographies was fashioned before moving on to argue that their final addressee was the Soviet state, that their content changed in line with political and ideological changes in the USSR, that the practice of writing them had much in common with Christian confession, and that the spread of this practice among millions of people functioned as a mechanism of subjectification aimed at “making them Soviet.”
Modeling cancer using patient-derived induced pluripotent stem cells to understand development of childhood malignancies
Authors: Marin Navarro Ana , Susanto Evelyn , Falk Anna , Wilhelm Margareta
Published: January 2018

In vitro modeling of complex diseases is now a possibility with the use of patient-derived induced pluripotent stem (iPS) cells. Their stem cell properties, including self-renewal and their potential to virtually differentiate into any cell type, emphasize their importance as a translational tool for modeling disorders that so far have been limited by the unavailability of primary cell lines, animal models, or inaccessible human materials. Around 100 genes with germline mutations have been described to be responsible for cancer predisposition. Familial cancers are usually diagnosed earlier in life since these patients already carry the first transforming hit. Deriving iPS cells from patients suffering from familial cancers provides a valuable tool for understanding the mechanisms underlying pediatric cancer onset and progression since they require less mutation recurrence than adult cancers to develop. At the same time, some familial mutations are found in sporadic cases and are a valuable prognostic tool. Patient-derived iPS cells from germline malignancies can also create new tools in developing specific drugs with more personalized-therapy strategies.
Legionella DotM structure reveals a role in effector recruiting to the Type 4B secretion system
Authors: Meir Amit , Chetrit David , Liu Luying , Roy Craig R. , Waksman Gabriel
Published: January 2018

Legionella pneumophila, a causative agent of pneumonia, utilizes the Type 4B secretion (T4BS) system to translocate over 300 effectors into the host cell during infection. T4BS systems are encoded by a large gene cluster termed dot/icm, three components of which, DotL, DotM, and DotN, form the “coupling complex”, which serves as a platform for recruitment of effector proteins. One class of effectors includes proteins containing Glu-rich/E-block sequences at their C terminus. However, the protein or region of the coupling complex mediating recruitment of such effectors is unknown. Here we present the crystal structure of DotM. This all alpha-helical structure exhibits patches of positively charged residues. We show that these regions form binding sites for acidic Glu-rich peptides and that mutants targeting these patches are defective in vivo in the translocation of acidic Glu-rich motif-containing effectors. We conclude that DotM forms the interacting surface for recruitment of acidic Glu-rich motif-containing Legionella effectors.
A roadmap towards personalized immunology
Authors: Delhalle Sylvie , Bode Sebastian F. N. , Balling Rudi , Ollert Markus , He Feng Q.
Published: January 2018

Big data generation and computational processing will enable medicine to evolve from a “one-size-fits-all” approach to precise patient stratification and treatment. Significant achievements using “Omics” data have been made especially in personalized oncology. However, immune cells relative to tumor cells show a much higher degree of complexity in heterogeneity, dynamics, memory-capability, plasticity and “social” interactions. There is still a long way ahead on translating our capability to identify potentially targetable personalized biomarkers into effective personalized therapy in immune-centralized diseases. Here, we discuss the recent advances and successful applications in “Omics” data utilization and network analysis on patients’ samples of clinical trials and studies, as well as the major challenges and strategies towards personalized stratification and treatment for infectious or non-communicable inflammatory diseases such as autoimmune diseases or allergies. We provide a roadmap and highlight experimental, clinical, computational analysis, data management, ethical and regulatory issues to accelerate the implementation of personalized immunology.
Author Correction: Interrogation of γ-tubulin alleles using high-resolution fitness measurements reveals a distinct cytoplasmic function in spindle alignment
Authors: Shulist Kristian , Yen Eric , Kaitna Susanne , Leary Allen , Decterov Alexandra , Gupta Debarun , Vogel Jackie
Published: January 2018

A correction to this article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.
Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach
Authors: Akberdin Ilya R. , Thompson Merlin , Hamilton Richard , Desai Nalini , Alexander Danny , Henard Calvin A. , Guarnieri Michael T. , Kalyuzhnaya Marina G.
Published: January 2018

Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.
Oxidized Carbon Black: Preparation, Characterization and Application in Antibody Delivery across Cell Membrane
Authors: Amornwachirabodee Kittima , Tantimekin Nattapol , Pan-In Porntip , Palaga Tanapat , Pienpinijtham Prompong , Pipattanaboon Chonlatip , Sukmanee Thanyada , Ritprajak Patcharee , Charoenpat Promchat , Pitaksajjakul Pannamthip , Ramasoota Pongrama , Wanichwecharungruang Supason
Published: January 2018

Modulating biomolecular networks in cells with peptides and proteins has become a promising therapeutic strategy and effective biological tools. A simple and effective reagent that can bring functional proteins into cells can increase efficacy and allow more investigations. Here we show that the relatively non-toxic and non-immunogenic oxidized carbon black particles (OCBs) prepared from commercially available carbon black can deliver a 300 kDa protein directly into cells, without an involvement of a cellular endocytosis. Experiments with cell-sized liposomes indicate that OCBs directly interact with phospholipids and induce membrane leakages. Delivery of human monoclonal antibodies (HuMAbs, 150 kDa) with specific affinity towards dengue viruses (DENV) into DENV-infected Vero cells by OCBs results in HuMAbs distribution all over cells’ interior and effective viral neutralization. An ability of OCBs to deliver big functional/therapeutic proteins into cells should open doors for more protein drug investigations and new levels of antibody therapies and biological studies.
Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid
Authors: Mendes Niege S. , Bitencourt Tamires A. , Sanches Pablo R. , Silva-Rocha Rafael , Martinez-Rossi Nilce M. , Rossi Antonio
Published: January 2018

While fatty acids are known to be toxic to dermatophytes, key physiological aspects of the Trichophyton rubrum response to undecanoic acid (UDA), a medium chain saturated fatty acid (C11:0), are not well understood. Thus, we analysed RNA-seq data from T. rubrum exposed to sub-lethal doses of UDA for 3 and 12 h. Three putative pathways were primarily involved in UDA detoxification: lipid metabolism and cellular membrane composition, oxidative stress, and pathogenesis. Biochemical assays showed cell membrane impairment, reductions in ergosterol content, and an increase in keratinolytic activity following UDA exposure. Moreover, we assessed differential exon usage and intron retention following UDA exposure. A key enzyme supplying guanine nucleotides to cells, inosine monophosphate dehydrogenase (IMPDH), showed high levels of intron 2 retention. Additionally, phosphoglucomutase (PGM), which is involved in the glycogen synthesis and degradation as well as cell wall biosynthesis, exhibited a significant difference in exon 4 usage following UDA exposure. Owing to the roles of these enzymes in fungal cells, both have emerged as promising antifungal targets. We showed that intron 2 retention in impdh and exon 4 skipping in pgm might be related to an adaptive strategy to combat fatty acid toxicity. Thus, the general effect of UDA fungal toxicity involves changes to fungal metabolism and mechanisms for regulating pre-mRNA processing events.
A Longitudinal Investigation of Preferential Attention to Biological Motion in 2- to 24-Month-Old Infants
Authors: Sifre Robin , Olson Lindsay , Gillespie Scott , Klin Ami , Jones Warren , Shultz Sarah
Published: January 2018

Preferential attention to biological motion is an early-emerging mechanism of adaptive action that plays a critical role in social development. The present study provides a comprehensive longitudinal mapping of developmental change in preferential attention to biological motion in 116 infants at 7 longitudinal time points. Tested repeatedly from 2 until 24 months of age, results reveal that preferential attention to biological motion changes considerably during the first months of life. Previously reported preferences in both neonates and older infants are absent in the second month but do reemerge by month 3 and become increasingly pronounced during the subsequent two years. These results highlight the second month of life as a potentially critical transition period in social visual engagement.
Anthropometry-based estimation of body heat capacity in individuals aged 7–69 years: the Size Korea Survey 2010
Authors: Pham Duong Duc , Lee Jeong Hoon , Kim Ka Yul , Song Ji Yeon , Kim Ji Eun , Leem Chae Hun
Published: January 2018

Although our previously developed anthropometry-based calculation of heat capacity (HC) for adults appeared to be precise and valid, its use in children and adolescents may be associated with bias. This study investigated a large dataset from the Size Korea survey, a national anthropometric survey conducted in 2010, to revalidate our previous HC equation and to develop another one that is appropriate for children and adolescents. We enrolled 12,766 participants aged 7–69 years with body composition data measured by multi-frequency bioelectrical impedance analysis. Age was associated with HC in children aged 7–19 years (R2 = 0.58) but not in adults (R2 = 0.007). Linear regression was appropriate to describe the relationship between HC and body surface area (BSA) in adults, whereas the regression in children and adolescent was quadratic. The previously developed HC equation had high reliability (intra-class correlation coefficient = 0.995) and predictive power (accurate prediction rate = 86.1%) in the >20 age group. The model composed of sex, body weight, BSA, and BSA2 was appropriate for the prediction of HC in young individuals aged 7–19 years. In conclusion, anthropometric-based modelling is a simple, reliable, and useful method for the calculation of HC.
Practical immune-barometer sensor for trivalent chromium ion detection using gold core platinum shell nanoparticle probes
Authors: Xiao Meng , Shen Haicong , Fu Qiangqiang , Xiao Wei , Bian Hongfen , Zhang Zhigang , Tang Yong
Published: January 2018

Schematic of an immune-barometer sensor, including a digital barometer and a competitive immunoassay reaction system.
Tracking HOCl concentrations across cellular organelles in real time using a super resolution microscopy probe
Authors: Ali Firoj , Aute Sunil , Sreedharan Sreejesh , Anila H. A. , Saeed Hiwa K. , Smythe Carl G. , Thomas Jim A. , Das Amitava
Published: January 2018

A probe that specifically images HOCl in Golgi apparatus and lysosomes that is compatible wih the super resolution microscopy technique, SIM, is reported.