bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep center related to hydrogen and carbon in p-type silicon
Authors: Kamiura Yoichi , Tsutsue Makoto , Yamashita Yoshifumi , Hashimoto Fumio , Okuno Kazuhiko 
Published: July 2002

We have found a hole trap related to hydrogen and carbon in p-type crystalline silicon after hydrogen and deuterium injection by chemical etching and plasma exposure. It was found from deep-level transient spectroscopy that this center is located at 0.33 eV above the valence band and shows no Poole–Frenkel effect in electric fields lower than 6×103 V/cm. The depth profiling technique using deep-level transient spectroscopy indicated that this center is distributed over the range 1–7 μm from the surface with densities of 1011–1013 cm−3, depending on the hydrogenation method. On the other hand, secondary ions mass spectroscopy revealed that the majority of deuterium injected into silicon exists within a much shallower region less than 60 nm from the surface with higher densities of 1018–1020 cm−3. We have therefore concluded that the majority of injected hydrogen stays in the near-surface region probably in the form of a molecule and larger clusters and only the minority diffuses into the bulk in an atomic form to form an electrically active complex with carbon. We performed annealing experiments to investigate the thermal stability of the complex. It was stable in the dark up to 100 °C, above which it was completely annihilated in first-order kinetics with an activation energy of about 1.7 eV. The illumination of band gap light with and without a reverse bias at room temperature and at 50 °C induced no effect on the stability of the trap. This is contrast to the photoinduced annihilation of a recently observed electron trap related also to hydrogen and carbon and with comparable thermal stability in n-type silicon.
These similarities and differences between the two traps and the comparison of the present results with the recently published theoretical calculations of the total energy of hydrogen configurations in the hydrogen-carbon complex suggest that the previously observed electron trap and the presently observed hole trap arise from two different defects with similar origins and structures and are tentatively ascribed to the electronic states of ‘‘bond-centered’’ and ‘‘anti-bonding of carbon’’ configurations of hydrogen in the hydrogen-carbon complex, respectively.
Liver cirrhosis mortality trends in Eastern Europe, 1970–1989. Analyses of age, period and cohort effects and of latency with alcohol consumption
Authors: Corrao Giovanni 
Published: July 2002

AbstractThere is evidence that in some Eastern European countries alcohol‐related deaths have an important impact on mortality. In the whole European population increasing trends in mortality were observed until the second half of the 1970s, followed by a decline in the following decades. By contrast, in Eastern Europe continuously rising trends have been observed. The aim of the present study is to describe cirrhosis mortality trends in Eastern European countries between 1970 and 1989. This is a descriptive study in seven European countries, compared with Europe as a whole. A Poisson's log‐linear age‐period‐cohort model is used to ascertain whether the recent trend in mortality represents a short‐term fluctuation or an emerging long‐term trend. In addition, changes in cirrhosis death rates were regressed onto changes in per capita alcohol consumption (1961–89) in order to evaluate the latency period between trends. The birth‐cohort effects suggested that in Eastern Europe as a whole, and in particular in Hungary, Bulgaria and Romania, the mortality will probably increase in the next decade. Eastern European countries showed a latency period between trends in alcohol consumption and in mortality rates of many years, whereas in Europe as a whole the cirrhosis mortality rates were explained by their relationship with per capita alcohol consumption which lagged by only a few years. Further increases in cirrhosis mortality, and probably in other alcohol‐related problems, are expected in several Eastern European countries. Epidemiological studies aimed to estimate the proportion of disease attributable to known risk factors of cirrhosis, and monitoring programmes of viral infections and of alcohol consumption and alcohol‐related problems, should be implemented to address the planning of public health programmes.
Purification and Characterization of an Extracellular Serine Proteinase from Acanthamoeba castellanii
Authors: Cho Jung‐Hwa , Na Byoung‐Kuk , Kim Tong‐Soo , Song Chul‐Yong 
Published: July 2002

AbstractAn extracellular proteinase of Acanthamoeba castellanii was purified and its biochemical and pathological properties were characterized. The molecular mass of the purified enzyme was ˜ 42 kDa as estimated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and Sephacryl S‐200 HR gel‐filtration chromatography. Therefore, its structure seemed to be monomeric with a single polypeptide. Its activity was inhibited by the serine proteinase inhibitors diisopropyl fluorophosphate and phenylmethanesulfonyl fluoride. Its activity was optimum at 30 to 50 °C with a maximum at 50 °C; optimal pH was 8.0. As much as 70% of the enzyme activity was maintained at 50 °C for at least 12 h but was rapidly inactivated thereafter. The purified enzyme degraded collagen and rabbit corneal extract. Furthermore, it exhibited strong cytopathic effects on human corneal epithelial cells and fibroblast cells. These suggest the possible role of this enzyme in the pathogenesis of Acanthamoeba.
SSMAL: similarity searching with alignment graphs.
Authors: Nicod√®me P 
Published: July 2002

Abstract
MOTIVATION: We want to provide biologists with a fast and sensitive scanning tool for searching local alignments of a protein query sequence against databases of protein multiple alignments, such as ProDom. Conversely, we want to provide a tool for locally aligning a protein multiple alignment query against a protein database such as SWISSPROT. RESULTS: We developed the program SSMAL (Shuffling Similarities with Multiple Alignments) which utilizes features of the Blast (Altschul et al., J. Mol. Biol., 215, 403-410, 1990) algorithm and part of the Blast code. Our software allows both scanning of multiple alignments and searching with a multiple alignment. Deletions in the multiple alignment only are handled and a SSMAL search may miss some similarities found by a profile search. However, an SSMAL scan of a database such as ProDom would be 20-30 times faster that a profile scan. In the worst case, a SSMAL search is approximately 9 times faster than a profile search. AVAILABILITY: http://www.dkfz-heidelberg.de/tbi/ people/nicodeme and follow the hyperlink SSMAL. CONTACT: p.nicodeme@DKFZ-Heidelberg.de
A model system for studying the integration of molecular biology databases.
Authors: Macauley J , Wang H , Goodman N 
Published: July 2002

Abstract
MOTIVATION: Integration of molecular biology databases remains limited in practice despite its practical importance and considerable research effort. The complexity of the problem is such that an experimental approach is mandatory, yet this very complexity makes it hard to design definitive experiments. This dilemma is common in science, and one tried-and-true strategy is to work with model systems. We propose a model system for this problem, namely a database of genes integrating diverse data across organisms, and describe an experiment using this model. RESULTS: We attempted to construct a database of human and mouse genes integrating data from GenBank and the human and mouse genome-databases. We discovered numerous errors in these well-respected databases: approximately 15% of genes are apparently missing from the genome-databases; links between the sequence and genome-databases are missing for another 5-10% of the cases; about a third of likely homology links are missing between the genome-databases; 10-20% of entries classified as 'genes' are apparently misclassified. By using a model system, we were able to study the problems caused by anomalous data without having to face all the hard problems of database integration. CONTACT: nat@jax.org
A new method to predict the consensus secondary structure of a set of unaligned RNA sequences.
Authors: Bouthinon D , Soldano H 
Published: July 2002

Abstract
MOTIVATION: To predict the consensus secondary structure, possibly including pseudoknots, of a set of RNA unaligned sequences. RESULTS: We have designed a method based on a new representation of any RNA secondary structure as a set of structural relationships between the helices of the structure. We refer to this representation as a structural pattern. In a first step, we use thermodynamic parameters to select, for each sequence, the best secondary structures according to energy minimization and we represent each of them using its corresponding structural pattern. In a second step, we search for the repeated structural patterns, i.e. the largest structural patterns that occur in at least one sequence, i.e. included in at least one of the structural patterns associated to each sequence. Thanks to an efficient encoding of structural patterns, this search comes down to identifying the largest repeated word suffixes in a dictionary. In a third step, we compute the plausibility of each repeated structural pattern by checking if it occurs more frequently in the studied sequences than in random RNA sequences. We then suppose that the consensus secondary structure corresponds to the repeated structural pattern that displays the highest plausibility. We present several experiments concerning tRNA, fragments of 16S rRNA and 10Sa RNA (including pseudoknots); in each of them, we found the putative consensus secondary structure.
Sequence-structure specificity of a knowledge based energy
function at the secondary structure level
Authors: Xu Dong , Unseren Michael A. , Xu Ying , Uberbacher Edward C. 
Published: July 2002

Abstract
*To whom correspondence should be addressed.
Motivation: This paper investigates the sequence-structure specificity of a representative knowledge based energy function by applying it to threading at the level of secondary structures of proteins. Assessing the strengths and weaknesses of an energy function at this fundamental level provides more detailed and insightful information than at the tertiary structure level and the results obtained can be useful in tertiary level threading.
Results: We threaded each of the 293 non-redundant proteins onto the secondary structures contained in its respective native protein (host template). We also used 68 pairs of proteins with similar folds and low sequence identity. For each pair, we threaded the sequence of one protein onto the secondary structures of the other protein. The discerning power of the total energy function and its one-body, pairwise, and mutation components is studied. We then applied our energy function to a recent study which demonstrated how a designed 11-amino acid sequence can replace distinct segments (one segment is an α-helix, the other is a β-sheet) of a protein without changing its fold. We conducted random mutations of the designed sequence to determine the patterns for favorable mutations. We also studied the sequence-structure specificity at the boundaries of a secondary structure. Finally, we demonstrated how to speed up tertiary level threading by filtering out alignments found to be energetically unfavorable during the secondary structure threading.
Availability: The program is available on request from the authors.
Contact: xud@ornl.gov
Reducing Optical Reflection Loss for Perovskite Solar Cells Via Printable Mesoporous SiO2 Antireflection Coatings
Authors: Wang Xiadong , Wang Wei , Liu Jiale , Qi Jianhang , He Yue , Wang Yifan , Hu Wenjing , Cheng Yanjie , Chen Kai , Hu Yue , Mei Anyi , Han Hongwei 
Published: August 2022

AbstractThe power conversion efficiency (PCE) of single‐junction perovskite solar cells (PSCs) is being rapidly promoted towards their theoretical limit, with a certified value of 25.7%. Reducing optical loss will further contribute to PCE improvement. Here, the optical loss including reflection loss, absorption loss, and transmission loss in printable mesoscopic perovskite solar cells (p‐MPSCs) is analyzed. A printable mesoporous SiO2 antireflection coating for improving the transmittance of the fluorine‐doped tin oxide (FTO) glass substrate by reducing optical reflection at the air/glass interface is reported. With modulated porosity and thickness, the mesoporous SiO2 film constructs a graded refractive index interface and increases the transmittance of FTO glass by ≈2%–4% in the spectral range of 350–800 nm at normal incident angle with the highest transmittance improved from 85% to 89%. The SiO2 coating also exhibits wide‐angle and broadband antireflection properties. The coatings successfully help p‐MPSCs obtain about an average 3% enhancement in the short‐circuit current density (JSC) and PCE. This study demonstrates the necessity of optical management for efficient solar cells and provides a cost‐effective and scalable antireflection coating for the future realistic application of PSCs.
Hollow Cu2O@CoMn2O4 Nanoreactors for Electrochemical NO Reduction to NH3: Elucidating the Void‐Confinement Effects on Intermediates
Authors: Bai Chunpeng , Fan Shiying , Li Xinyong , Niu Zhaodong , Wang Jing , Liu Zhiyuan , Zhang Dongke 
Published: August 2022

AbstractHollow nanoreactors show great potential in catalysis due to the void‐confinement effect. Yet few studies have investigated the void‐confinement effect of hollow nanoreactors on intermediates. Herein, electrochemical NO reduction to NH3 (ENOR) is used as a probe reaction to study the void‐confinement effect of hollow Cu2O@CoMn2O4 nanoreactors on intermediates. Combined with the results of catalytic activity, H2‐treated in situ diffusion Fourier transform infrared spectroscopy and the finite‐element method simulation confirm that the void‐confinement effect on the intermediate is the main reason for enhanced ENOR efficiency. Additionally, theoretical calculations also show that the Cu sites of Cu2O@CoMn2O4 nanoreactors are favorable for the formation of *NOH intermediates. This work not only gives an insight into void‐confinement effect of hollow nanoreactors on intermediates but also provides a valuable strategy for improving ENOR.
Interstitial Photothermal Therapy Generates Durable Treatment Responses in Neuroblastoma
Authors: Ledezma Debbie K. , Balakrishnan Preethi B. , Shukla Anshi , Medina Jacob A. , Chen Jie , Oakley Emily , Bollard Catherine M. , Shafirstein Gal , Miscuglio Mario , Fernandes Rohan 
Published: August 2022

AbstractPhotothermal therapy (PTT) represents a promising modality for tumor control typically using infrared light‐responsive nanoparticles illuminated by a wavelength‐matched external laser. However, due to the constraints of light penetration, PTT is generally restricted to superficially accessible tumors. With the goal of extending the benefits of PTT to all tumor settings, interstitial PTT (I‐PTT) is evaluated by the photothermal activation of intratumorally administered Prussian blue nanoparticles with a laser fiber positioned interstitially within the tumor. This interstitial fiber, which is fitted with a terminal diffuser, distributes light within the tumor microenvironment from the “inside‐out” as compared to from the “outside‐in” traditionally observed during superficially administered PTT (S‐PTT). I‐PTT improves the heating efficiency and heat distribution within a target treatment area compared to S‐PTT. Additionally, I‐PTT generates increased cytotoxicity and thermal damage at equivalent thermal doses, and elicits immunogenic cell death at lower thermal doses in targeted neuroblastoma tumor cells compared to S‐PTT. In vivo, I‐PTT induces significantly higher long‐term tumor regression, lower rates of tumor recurrence, and improved long‐term survival in multiple syngeneic murine models of neuroblastoma. This study highlights the significantly enhanced therapeutic benefit of I‐PTT compared to traditional S‐PTT as a promising treatment modality for solid tumors.
Mimicking Bone Extracellular Matrix: From BMP‐2‐Derived Sequences to Osteogenic‐Multifunctional Coatings
Authors: Oliver‐Cervelló Lluís , Martin‐Gómez Helena , Mandakhbayar Nandin , Jo Young‐Woo , Cavalcanti‐Adam Elisabetta Ada , Kim Hae‐Won , Ginebra Maria‐Pau , Lee Jung‐Hwan , Mas‐Moruno Carlos 
Published: August 2022

AbstractCell–material interactions are regulated by mimicking bone extracellular matrix on the surface of biomaterials. In this regard, reproducing the extracellular conditions that promote integrin and growth factor (GF) signaling is a major goal to trigger bone regeneration. Thus, the use of synthetic osteogenic domains derived from bone morphogenetic protein 2 (BMP‐2) is gaining increasing attention, as this strategy is devoid of the clinical risks associated with this molecule. In this work, the wrist and knuckle epitopes of BMP‐2 are screened to identify peptides with potential osteogenic properties. The most active sequences (the DWIVA motif and its cyclic version) are combined with the cell adhesive RGD peptide (linear and cyclic variants), to produce tailor‐made biomimetic peptides presenting the bioactive cues in a chemically and geometrically defined manner. Such multifunctional peptides are next used to functionalize titanium surfaces. Biological characterization with mesenchymal stem cells demonstrates the ability of the biointerfaces to synergistically enhance cell adhesion and osteogenic differentiation. Furthermore, in vivo studies in rat calvarial defects prove the capacity of the biomimetic coatings to improve new bone formation and reduce fibrous tissue thickness. These results highlight the potential of mimicking integrin‐GF signaling with synthetic peptides, without the need for exogenous GFs.
Mechanistic Insights of Electrochemical Cl2 and O2 Generation from Lanthanum Cobalt Manganese Oxide
Authors: Sood Kritika , Rana Supriya , Wadhwa Ritika , Bhasin Kuldeep Kumar , Jha Menaka 
Published: August 2022

AbstractThe chlorine evolution reaction holds a core role in the chemical industries and water‐treatment plants. To overcome the high power input supplied for Cl2 generation at an industrial scale an efficient and durable electrocatalyst is always on hunt. Double perovskite oxides have been used previously for oxygen evolution reaction (OER) and have shown outstanding results on the ground of dual surface active site mechanism. Here, La2CoMnO6 (LCMO) are explored for the electrochemical Cl2 and O2 generation. The electrocatalytic studies are performed in 5 m NaCl (pH ≈ 2.2) for chlorine evolution reaction (CER) and 1 m KOH (pH = 13.5) for OER. The LCMO shows enhanced catalytic activity with onset and overpotential of 75 and 280 mV for CER. Further, the kinetics of the catalytic reaction is determined by the Tafel slope values that is calculated to be 44 mV dec−1 for CER. The interfacial charge transfer resistance value at 11 Ω tells the insight mechanism by facilitating more interaction between electrode‐electrolyte interfaces. In addition to this, wettability analysis of LCMO shows a contact angle as low as 23°. The present study paves a way for double perovskites to be used as an electro‐catalyst for the chlor‐alkali process.
Zincate‐Mediated Remote Functionalisation of p‐Iodobenzyl Derivatives Through Metallotropy in 2‐Methyltetrahydrofuran as Key Solvent
Authors: Pierret Alexandre , Denhez Clément , Gros Philippe C. , Vasseur Alexandre 
Published: August 2022

Abstract2‐MeTHF (2‐methyltetrahydrofuran) promotes the zincate‐mediated remote functionalisation of p‐iodobenzyl derivatives through metallotropy with a broad scope. This biosourced solvent remarkably impacted all the key elementary steps involved in the tandem reaction. The method tolerates a wide range of sensitive functionalities within the substrates as well as enolisable and activated or deactivated aromatic aldehydes as reaction partners. A challenging benzyl naphthalene derivative was even reacted through an original dearomatisation/rearomatisation/metallotropy chain.magnified image
Enzyme activities as soil health indicators in relation to soil characteristics and crop production
Authors: Sainju Upendra M. , Liptzin Daniel , Dangi Sadikshya M. 
Published: August 2022

AbstractSoil enzyme activities are known for early indicators of soil health but have not been related to most soil properties and crop yields. We examined the relationships among activities of four soil enzymes (β‐glucosidase [BG], N‐acetyl‐β‐glucosaminidase [NAG], arylsulfatase [AST], and phosphomonoesterase [PME]), 62 soil properties, and mean crop yields in two long‐term (14‐ and 36‐yr‐old) dryland farming sites in the northern Great Plains, USA. Treatments were no‐till and till crop rotations with spring wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), pea (Pisum sativum L.), and fallow with and without N fertilization. Soil samples collected before farming operations in April 2019 were analyzed for physical, chemical, biological, and biochemical properties and mean crop yields were determined. The principal component analysis (PCA) showed that BG was associated to most soil physical, chemical, biological, and biochemical properties followed by NAG and PME at both sites. The AST was associated to limited number of soil properties. The BG related to mean crop yield across years in one site and NAG related to yields in both sites, but AS and PME were not related to yields. Because of the greater sensitivity to cropping systems and relationships with most soil properties and long‐term crop yields, BG and NAG activities may be considered as promising soil health indicators compared with other enzyme activities under dryland cropping systems in the northern Great Plains.
Concurrent improvement of durum and emmer wheat through reciprocal backcrossing and hybridization
Authors: Shoormij Fatemeh , Mirlohi Aghafakhr , Saeidi Ghodratollah , Mohammadi Majid 
Published: August 2022

AbstractEmmer wheat has not been improved but is a valuable gene source for improving durum (Triticum turgidum ssp. durum). Conversely, durum is less looked upon for emmer (T. turgidum ssp. dicoccum) improvement. This study examined the possibility of concurrently improving the two species by crossing eight durum cultivars with four emmer local varieties in a half‐diallel fashion in two consecutive years. Also, emmer and two durum genotypes were reciprocally backcrossed, and their BC1F1 progeny were field‐evaluated during the wheat cropping season (November–June) at the Isfahan University of Technology research farm (32°32′ N, 51°23′ E). The results showed that durum wheat had a considerable effect on the grain yield (GY), kernel diameter, 1,000‐kernel weight (TKW), and test weight of F1 hybrids, whereas emmer contributed more to increasing the grain protein content (GPC), kernel length, and plant height (PH). A similar pattern was observed for BC1F1 hybrids from the two recurrent durum parents. The GPC was reduced with recurrent durum parents in the backcrosses compared with emmer, but was still higher than in both durum parents. In the backcrosses with the recurrent emmer parent, GY and TKW were higher than those of emmer but only slightly lower than those of the durum parents. The PH was strongly influenced by emmer in all crosses, though the lodging was significantly reduced compared with emmer, possibly through obtaining stronger stems from durum. These findings suggest the possibility of combining desirable genes from the two species and their concurrent improvement in a single breeding program.