bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response to the comments of D. R. Blackman and Y. Peleg (JRA 14, 411-14)
Authors: Kessener Paul 
Published: September 2015

The comments on my article (JRA 13,104-32) by Blackman and Peleg, which are much appreciated, reflect prevailing discussions on Roman hydraulic engineering practices as well as on the relevant paragraphs of Vitruvius (8.6). Blackman focuses mainly on technical aspects, while Peleg aims at archaeological arguments.Blackman starts with a discussion of the term ‘siphon’, which he regrets being used as it could lead to misunderstanding: ‘siphon’ would represent a “real” siphon, not an “inverted” siphon, suggesting that I must have meant that there was a real siphon at Aspendos. However, in archaeology “siphon” is generally accepted to represent an inverted siphon. There is no misunderstanding: at Aspendos we have an inverted siphon, and since real siphons are not known in classical aqueduct systems, there is no objection to using ‘siphon’ and ‘inverted siphon’ for one and the same notion. Subsequently he states: “The presence of air pockets and so on is almost irrelevant to operations [of siphons] if no point in the system lies above the Hydraulic Gradient Line; were it not so, no garden hose would work reliably” This is a misconception. It is only due to the fact that our garden hoses are connected to supplies with elevated pressures that we get water from them. If we would connect the hose to a low-pressure source (e.g., to a rainwater container standing at ground level), we have to straighten out the coils before water will emerge. If the hose is coiled up, for example, on a wall support but positioned below the free water surface in the container to which it is connected, while we are holding the free end somewhere near the ground, we have nothing but an inverted siphon with high points. If air pockets are irrelevant, water should come out, but it does not if air is in the hose. For problems associated with air pockets in gravity-driven closed conduit systems (which classical siphons must be considered to be), see G. Corcos, Air in water pipes (1989) and H. T. Falvey, Air-water flow in hydraulic structures (1980).
The Severan coin hoard from Shapwick (JRA 14, 358-72): a comment
Authors: Reece Richard 
Published: September 2015

Since most coin hoards are found without any archaeological context, even when excavation after discovery is possible, prompt publication of a large hoard of denarii with its context is so unusual an event that a few extra comments and questions may be allowed.I have doubts about the comparison with the site at Frocester (Glos.). The finds there suggested the remains of an iron-bound chest, and it might be that that was a strong box. If so, it was a permanent feature but was found empty. The Shapwick hoard was deposited in a scoop in the ground and was presumably a temporary hiding-place for a sum of money which might be roughly £150,000 to £250,000 in modern terms. The hiding of the hoard would, in a sense, be more ‘normal’, and certainly more safe, if it were done within the walls of a derelict building rather than an active farm. From the archaeological details this seems to be a possibility.
Supplying the Roman fleet: native Belgic, Frisian and Germanic pottery from Cologne
Authors: Carroll Maureen 
Published: September 2015

In 1995/96 archaeological excavations were conducted at Cologne on the site known as the Alteburg where the base of the Rhine fleet (Classis Germanica) was located. The area investigated was located in the E part of the fort near the river bank (fig. 1). Stratigraphic excavations clarified the chronology of the site, revealing 8 different building phases and a much more complex history than had previously been realised. In Phases 1 (Tiberian), 2 (Claudian), and 3 (Vespasianic), the barracks of the fort were timber structures. Under Domitian after 90/91, these buildings were demolished (Phase 4), and the area levelled to be replaced in Phase 5 by new barrack blocks with stone socles and a timber superstructure. After a fire around the middle of the 2nd c., rebuilding took place in Phases 6 and 7, the remains of which were poorly preserved. In Phase 8, around 270-280, the fort was abandoned and the riverside ditch backfilled. Evidence also suggests that the site was first occupied under Tiberius by legionary troops, possibly Legio I and XX, with a contingent of ships, and that it was not until the establishment of the provincial fleet under Claudius that the site became the permanent operational base of the fleet.Fragments of native, handmade Roman pottery were found in the post trenches, layers and pit fills, ranging in date from the early 1st to the mid-2nd c. (figs. 2-3). Since much of this pottery is virtually unknown on the Lower Rhine in Germany, a study of it in this context can make an important contribution to Roman pottery studies. Furthermore, analysis of the pottery allows us to determine the provenances and better understand the interaction between the Roman military and native societies, particularly in regard to the role various regions played in supplying the fleet with provisions.
In search of Muziris
Authors: Gurukkal Rajan , Whittaker Dick 
Published: September 2015

The importance of Muziris in Roman trade with India does not need any underlining. The port on the Malabar coast of modern Kerala figures prominently in the descriptions of classical geographers, it receives mention in the earliest Tamil poems, and it has come into the news more recently through the publication of a Greek papyrus from Egypt. It is also clear from the amount of Roman silver and gold coin found in S India — which gives some substance to Roman estimates of money haemorrhaging out to India — and from the value of the eastern cargoes recorded coming into Egypt and Rome that the trade was neither casual nor modest. All this is well known and has been carefully studied. The oddity, or pity, is that, despite the many ports listed in ancient authors along some 600 km of the Malabar coast, not a single one has been identified for certain, and not one has produced any serious archaeological evidence of Roman contact. As for Muziris, the most important of them all, we have only a vague idea of where it was located.Almost every earlier study has placed Muziris at Kodungallur (Cranganore/Cranganur in its Europeanised form) at the mouth of the Periyar river and north of Kerala's main modern port of Kochi (Cochin) (fig. 1). That is reasonable enough. The Periyar is the greatest river in Kerala and runs down from the towering western ghats to the sea. But where exactly on the Periyar? Kodungallur is the name given to a large zone, incorporating a number of small towns of which Kodungallur itself is one, strung out along the road that runs north for several kilometres from the Periyar parallel to the coast and the inland waters of the river Pullut. But how certain is this, anyway? These were the questions we had in mind when a group of us decided to take a closer look at the evidence, both in the literature and on the ground. Ultimately, only an excavation can answer the questions for certain, but perhaps we could narrow down the options.
Problems in the diagnosis of discordant atrioventricular with concordant ventriculo-arterial connections: anatomical considerations, surgical management, and long-term outcome
Authors: Laux Daniela , Houyel Lucile , Bajolle Fanny , Raimondi Francesca , Boudjemline Younes , Bonnet Damien 
Published: September 2015

AbstractBackgroundDiscordant atrioventricular with concordant ventriculo-arterial connections is a rare cardiac defect. When isolated, the haemodynamics resemble transposition of the great arteries. In complex heart defects such as heterotaxy, haemodynamics guide the surgical approach.ObjectiveTo report a series of eight patients with discordant atrioventricular and concordant ventriculo-arterial connections focussing on anatomical and diagnostic difficulties, surgical management, and follow-up.MethodsA retrospective review was carried out from 1983 to 2013. Anatomical description was based on segmental analysis. Emphasis was placed on the venoatrial connections.ResultsSegmental arrangement was {I, D, S} in six patients, all with spiralling great vessels. There were two patients with parallel great vessels of whom one had {S, L, D} and the other had {S, L, A} arrangement. Of eight patients, five had heterotaxy syndrome. Median age at repair surgery was 1.4 years (with a range from 1.1 months to 8.1 years). The repair surgery finally performed was the atrial switch procedure in seven out of eight patients. The main post-operative complications were two cases of baffle obstruction and one sick sinus syndrome needing pacemaker implantation. There were two early post-operative deaths and six late survivors. Median follow-up was 4.2 years (with a range from 3.9 to 26.7 years) with good functional status in all survivors.DiscussionDiagnosing discordant atrioventricular with concordant ventriculo-arterial connections remains challenging. There are ongoing controversies about the definition of atrial morphology and heterotaxy syndrome animating the anatomic discussion of these complex heart defects. Haemodynamically, the atrial switch procedure is the surgical method of choice with an encouraging long-term follow-up despite rhythm disturbances and baffle obstruction.
Anomalous left coronary artery arising from the right pulmonary artery in association with coarctation of the aorta
Authors: Liang Xuecun , Wu Lin 
Published: September 2015

AbstractIn this study, we describe a very rare case of anomalous left coronary artery arising from the right pulmonary artery in association with coarctation of the aorta. A 3-month-old boy presented with refractory congestive heart failure since 20 days after birth. The initial echocardiography suggested the diagnosis of left coronary artery-to-right pulmonary artery fistula associated with coarctation; however, selective coronary angiography demonstrated the rare anomaly of the left coronary artery arising from the right pulmonary artery. Subsequently, he underwent successful transcatheter balloon angioplasty for aortic coarctation and surgical repair of left coronary artery re-implantation.
Diagenetic Evolution and Reservoir Quality of Sandstones in the North Alpine Foreland Basin: A Microscale Approach
Authors: Gross Doris , Grundtner Marie-Louise , Misch David , Riedl Martin , Sachsenhofer Reinhard F. , Scheucher Lorenz 
Published: September 2015

AbstractSiliciclastic reservoir rocks of the North Alpine Foreland Basin were studied focusing on investigations of pore fillings. Conventional oil and gas production requires certain thresholds of porosity and permeability. These parameters are controlled by the size and shape of grains and diagenetic processes like compaction, dissolution, and precipitation of mineral phases. In an attempt to estimate the impact of these factors, conventional microscopy, high resolution scanning electron microscopy, and wavelength dispersive element mapping were applied. Rock types were established accordingly, considering Poro/Perm data. Reservoir properties in shallow marine Cenomanian sandstones are mainly controlled by the degree of diagenetic calcite precipitation, Turonian rocks are characterized by reduced permeability, even for weakly cemented layers, due to higher matrix content as a result of lower depositional energy. Eocene subarkoses tend to be coarse-grained with minor matrix content as a result of their fluvio-deltaic and coastal deposition. Reservoir quality is therefore controlled by diagenetic clay and minor calcite cementation.Although Eocene rocks are often matrix free, occasionally a clay mineral matrix may be present and influence cementation of pores during early diagenesis. Oligo-/Miocene deep marine rocks exhibit excellent quality in cases when early cement is dissolved and not replaced by secondary calcite, mainly bound to the gas–water contact within hydrocarbon reservoirs.
Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody
Authors: Chandramouli Sumana , Ciferri Claudio , Nikitin Pavel A. , Caló Stefano , Gerrein Rachel , Balabanis Kara , Monroe James , Hebner Christy , Lilja Anders E. , Settembre Ethan C. , Carfi Andrea 
Published: September 2015

AbstractHuman cytomegalovirus (HCMV) poses a significant threat to immunocompromised individuals and neonates infected in utero. Glycoprotein B (gB), the herpesvirus fusion protein, is a target for neutralizing antibodies and a vaccine candidate due to its indispensable role in infection. Here we show the crystal structure of the HCMV gB ectodomain bound to the Fab fragment of 1G2, a neutralizing human monoclonal antibody isolated from a seropositive subject. The gB/1G2 interaction is dominated by aromatic residues in the 1G2 heavy chain CDR3 protruding into a hydrophobic cleft in the gB antigenic domain 5 (AD-5). Structural analysis and comparison with HSV gB suggest the location of additional neutralizing antibody binding sites on HCMV gB. Finally, immunoprecipitation experiments reveal that 1G2 can bind to HCMV virion gB suggesting that its epitope is exposed and accessible on the virus surface. Our data will support the development of vaccines and therapeutic antibodies against HCMV infection.
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules
Authors: Imai Hiroshi , Shima Tomohiro , Sutoh Kazuo , Walker Matthew L. , Knight Peter J. , Kon Takahide , Burgess Stan A. 
Published: September 2015

AbstractCytoplasmic dynein is a dimeric AAA+ motor protein that performs critical roles in eukaryotic cells by moving along microtubules using ATP. Here using cryo-electron microscopy we directly observe the structure of Dictyostelium discoideum dynein dimers on microtubules at near-physiological ATP concentrations. They display remarkable flexibility at a hinge close to the microtubule binding domain (the stalkhead) producing a wide range of head positions. About half the molecules have the two heads separated from one another, with both leading and trailing motors attached to the microtubule. The other half have the two heads and stalks closely superposed in a front-to-back arrangement of the AAA+ rings, suggesting specific contact between the heads. All stalks point towards the microtubule minus end. Mean stalk angles depend on the separation between their stalkheads, which allows estimation of inter-head tension. These findings provide a structural framework for understanding dynein’s directionality and unusual stepping behaviour.
Calcium-controlled conformational choreography in the N-terminal half of adseverin
Authors: Chumnarnsilpa Sakesit , Robinson Robert C. , Grimes Jonathan M. , Leyrat Cedric 
Published: September 2015

AbstractAdseverin is a member of the calcium-regulated gelsolin superfamily of actin-binding proteins. Here we report the crystal structure of the calcium-free N-terminal half of adseverin (iA1–A3) and the Ca2+-bound structure of A3, which reveal structural similarities and differences with gelsolin. Solution small-angle X-ray scattering combined with ensemble optimization revealed a dynamic Ca2+-dependent equilibrium between inactive, intermediate and active conformations. Increasing calcium concentrations progressively shift this equilibrium from a main population of inactive conformation to the active form. Molecular dynamics simulations of iA1–A3 provided insights into Ca2+-induced destabilization, implicating a critical role for the A2 type II calcium-binding site and the A2A3 linker in the activation process. Finally, mutations that disrupt the A1/A3 interface increase Ca2+-independent F-actin severing by A1–A3, albeit at a lower efficiency than observed for gelsolin domains G1–G3. Together, these data address the calcium dependency of A1–A3 activity in relation to the calcium-independent activity of G1–G3.
Database of host-pathogen and related species interactions, and their global distribution
Authors: Wardeh Maya , Risley Claire , McIntyre Marie Kirsty , Setzkorn Christian , Baylis Matthew 
Published: September 2015

AbstractInteractions between species, particularly where one is likely to be a pathogen of the other, as well as the geographical distribution of species, have been systematically extracted from various web-based, free-access sources, and assembled with the accompanying evidence into a single database. The database attempts to answer questions such as what are all the pathogens of a host, and what are all the hosts of a pathogen, what are all the countries where a pathogen was found, and what are all the pathogens found in a country. Two datasets were extracted from the database, focussing on species interactions and species distribution, based on evidence published between 1950–2012. The quality of their evidence was checked and verified against well-known, alternative, datasets of pathogens infecting humans, domestic animals and wild mammals. The presented datasets provide a valuable resource for researchers of infectious diseases of humans and animals, including zoonoses.
Resolution and contrast enhancement of subtractive second harmonic generation microscopy with a circularly polarized vortex beam
Authors: Tian Nian , Fu Ling , Gu Min 
Published: September 2015

AbstractWe extend the subtractive imaging method to label-free second harmonic generation (SHG) microscopy to enhance the spatial resolution and contrast. This method is based on the intensity difference between two images obtained with circularly polarized Gaussian and doughnut-shaped beams, respectively. By characterizing the intensity and polarization distributions of the two focused beams, we verify the feasibility of the subtractive imaging method in polarization dependent SHG microscopy. The resolution and contrast enhancement in different biological samples is demonstrated. This work will open a new avenue for the applications of SHG microscopy in biomedical research.
Surface Engineering of Triboelectric Nanogenerator with an Electrodeposited Gold Nanoflower Structure
Authors: Park Sang-Jae , Seol Myeong-Lok , Jeon Seung-Bae , Kim Daewon , Lee Dongil , Choi Yang-Kyu 
Published: September 2015

AbstractA triboelectric nanogenerator composed of gold nanoflowers is demonstrated. The proposed triboelectric nanogenerator creates electricity by contact-separation-based electrification between an anodic metal and a cathodic polymer. For the improvement of output power via the enlargement of the effective surface area in the anodic metal, gold nanoflowers that produce a hierarchical morphology at a micro-to-nano scale by electrodeposition are utilized. The hierarchical morphology is controlled by the applied voltage and deposition time. Even though the triboelectric coefficient of gold is inferior to those of other metals, gold is very attractive to make a flower-like structure by electrodeposition. Moreover, gold is stable against oxidation by oxygen in air. From a reliability and practicality point of view, the aforementioned stability against oxidation is preferred.
Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB
Authors: Zuo Zhicheng , Wang Beibei , Weng Jingwei , Wang Wenning 
Published: September 2015

AbstractAcrB is the inner membrane transporter of the tripartite multidrug efflux pump AcrAB-TolC inE. coli, which poses a major obstacle to the treatment of bacterial infections. X-ray structures have identified two types of substrate-binding pockets in the porter domains of AcrB trimer: the proximal binding pocket (PBP) and the distal binding pocket (DBP) and suggest a functional rotating mechanism in which each protomer cycles consecutively through three distinct conformational states (access, binding and extrusion). However, the details of substrate binding and translocation between the binding pockets remain elusive. In this work, we performed atomic simulations to obtain the free energy profile of the translocation of an antibiotic drug doxorubicin (DOX) inside AcrB. Our simulation indicates that DOX binds at the PBP and DBP with comparable affinities in the binding state protomer and overcomes a 3 kcal/mol energy barrier to transit between them. Obvious conformational changes including closing of the PC1/PC2 cleft and shrinking of the DBP were observed upon DOX binding in the PBP, resulting in an intermediate state between the access and binding states. Taken together, the simulation results reveal a detailed stepwise substrate binding and translocation process in the framework of functional rotating mechanism.
A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β0-thalassaemia deletion
Authors: Leng Kho Siew , Heng Chua Kek , George Elizabeth , Tan Jin Ai Mary Anne 
Published: September 2015

AbstractHomozygosity for the α-thalassaemia Southeast Asian (α-SEA) and Filipino β0-thalassaemia (β-FIL) deletions can cause serious complications leading to foetal death or life-long blood transfusions. A rapid and accurate molecular detection assay is essential in populations where the deletions are common. In this study, gap-polymerase chain reaction (PCR) with high resolution melting (HRM) analysis was developed to detect both the large deletions. Melting curves at 86.9 ± 0.1 °C were generated by normal individuals without the α-SEA deletion, 84.7 ± 0.1 °C by homozygous α-SEA deletion individuals and two melting curves at 84.7 ± 0.1 °C and 86.9 ± 0.1 °C by α-SEA deletion carriers. Normal individuals without the β-FIL deletion produce amplicons with a melting temperature (Tm) at 74.6 ± 0.1 °C, homozygous β-FIL individuals produce amplicons with Tm at 73.6 ± 0.1 °C and heterozygous β-FIL individuals generate two amplicons with Tm at 73.6 ± 0.1 °C and 74.6 ± 0.1 °C. Evaluation using blinded tests on 220 DNA samples showed 100% sensitivity and specificity. The developed assays are sensitive and specific for rapid molecular and prenatal diagnosis for the α-SEA and β-FIL deletions.
Hong-Ou-Mandel Interference with a Single Atom
Authors: Ralley K. A. , Lerner I. V. , Yurkevich I. V. 
Published: September 2015

AbstractThe Hong-Ou-Mandel (HOM) effect is widely regarded as the quintessential quantum interference phenomenon in optics. In this work we examine how nonlinearity can smear statistical photon bunching in the HOM interferometer. We model both the nonlinearity and a balanced beam splitter with a single two-level system and calculate a finite probability of anti-bunching arising in this geometry. We thus argue that the presence of such nonlinearity would reduce the visibility in the standard HOM setup, offering some explanation for the diminution of the HOM visibility observed in many experiments. We use the same model to show that the nonlinearity affects a resonant two-photon propagation through a two-level impurity in a waveguide due to a “weak photon blockade” caused by the impossibility of double-occupancy and argue that this effect might be stronger for multi-photon propagation.