bluuebunny/crossref_metadata_2025_split huggingface dataset:
Existence for dislocation-free finite plasticity
Authors: Stefanelli Ulisse 
Published: February 2018

This note addresses finite plasticity under the constraint that plastic deformations are compatible. In this case, the total elastoplastic deformation of the medium is decomposed asy=ye○yp, where the plastic deformationypis defined on the fixed reference configuration and the elastic deformationyeis a mapping from the varying intermediate configurationyp(Ω). Correspondingly, the energy of the medium features both Lagrangian (plastic, loads) and not Lagrangian contributions (elastic).We present a variational formulation of the static elastoplastic problem in this setting and show that a solution is attained in a suitable class of admissible deformations. Possible extensions of the result, especially in the direction of quasistatic evolutions, are also discussed.
Increased Total Hip Arthroplasty Utilization, Osteoarthritis Diagnoses, and Comorbidity Burden in Patients Younger Than the Age of 65 Years: National Inpatient Trends 1998 to 2013
Authors: Brigati David , Navale Suparna , Schiltz Nicholas , Bozic Kevin 
Published: February 2018

AbstractPrimary total hip arthroplasty (THA) in patients younger than the age of 65 years demands long-term success to minimize lifetime revision surgery risks. Age at implantation, etiology of arthrosis, and comorbidity burden all have associations with revision risk. This study uses Nationwide Inpatient Sample (NIS) data between 1998 and 2013 to (1) report the annual utilization of THA in patients age 18 to 99 years divided into age groups, (2) determine trends in primary diagnoses, and (3) explore Elixhauser comorbidity burden trends. The authors reviewed 5,174,020 THA cases from the NIS. Cases were divided into age groups: 18 to 24, 25 to 34, 35 to 44, 45 to 54, 55 to 64, and 65 to 99 years. The annual utilization rate, primary diagnoses, and average count of Elixhauser comorbidities were plotted. Mann–Kendall's nonparametric tests determined significance with p < 0.05. The mean utilization of primary THA in patients aged 18 to 64 years was 57 cases per 105 persons (cpp). The incidence of utilization increased rapidly in patients age 55 to 64 years (123–240 cpp, p < 0.001) and age 45 to 54 years (46–100 cpp, p < 0.001). The predominant diagnoses were osteoarthritis increasing from 65 to 83% (p < 0.001), avascular necrosis decreasing from 17 to 7% (p < 0.001), and trauma decreasing from 11 to 6% (p < 0.001). The average count of Elixhauser comorbidities increased in all age groups from a minimum of 58% (1.2–1.9, p < 0.001) in patients age 55 to 64 years to a maximum of 200% (0.4–1.2, p = 0.003) in patients age 18 to 24 years. Increases in primary THA utilization are occurring disproportionately among patients age 45 to 64 years. The trends in etiologies and comorbidities show mixed anticipated effects on the risks for revision. Increased osteoarthritis diagnoses may be favorable as the etiology with the longest relative implant survival. However, increasing comorbidities may unfavorably heighten the risks of revision. Primary THA utilization is increasing for patients younger than the age of 65 years with osteoarthritis and rising comorbidity burdens. Current national administrative databases add valuable insights to large THA trends, but lack the granularity to fully characterize the causes behind revisions of primary THA.
Complex Pelvic Reconstruction using Patient-Specific Instrumentation and a 3D-Printed Custom Implant following Tumor Resection
Authors: Hennessy David , Anderson Megan , Lozano-Calderón Santiago 
Published: February 2018

AbstractResection of a periacetabular sarcoma is a difficult surgical problem due to the complex bony and soft tissue anatomy. The challenge of pelvic tumor resection lies in achieving clear margins while also reconstructing the defect with a durable construct. Limb salvage surgery involving these types of tumors, as well as other tumors of the pelvis, has made great progress recently due to remarkable technological innovation in the field of computer-assisted surgery and custom implant design. In this study, the authors review the case of a 9-year-old child with an osteosarcoma arising from the proximal femur with local spread into the hip joint and a skip metastasis in the ipsilateral acetabulum. They undertook limb-sparing extra-articular resection of the sarcoma with a reconstruction consisting of a 3D-custom printed pelvic implant and a proximal femur extendible prosthesis. The resection of the pelvis was performed with patient-specific cutting guides, rather than computer-assisted navigation. The resection resulted in a clear margin and the patient has had no evidence of local recurrence. These patient-specific guides closely matched the planned resection in terms of orientation in the pelvis, which allowed for straightforward implantation of the custom prosthesis at the time of surgery. The result has been a durable reconstruction that has produced an excellent functional outcome for this patient.
Generic assembly patterns in complex ecological communities
Authors: Barbier Matthieu , Arnoldi Jean-François , Bunin Guy , Loreau Michel 
Published: February 2018

Significance
Biodiversity may lead to the emergence of simple and robust relationships between ecosystem properties. Here we show that a wide range of models of species dynamics, in the limit of high diversity, exhibit generic behavior predictable from a few emergent parameters, which control ecosystem functioning and stability. Our work points toward ways to tackle the staggering complexity of ecological systems without relying on empirically unavailable details of their structure.
Cryo-EM reconstruction of AlfA from
Bacillus subtilis
reveals the structure of a simplified actin-like filament at 3.4-Å resolution
Authors: Szewczak-Harris Andrzej , Löwe Jan 
Published: February 2018

Significance
Protein filaments perform a vast array of functions inside almost all living cells. Actin-like proteins in archaea and bacteria have previously been found to form a surprising diversity of filament architectures, reflecting their divergent cellular roles. Actin-like AlfA is unique in that it is much smaller than all other filament forming actin-like proteins. With an atomic structure of the AlfA filament, obtained by high-resolution electron cryo-microscopy, we have revealed—at near-atomic level of detail—how AlfA filaments form dynamic filaments capable of transporting plasmid DNA in cells and how these filaments arrange into antiparallel bundles required for the segregation mechanism.
CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles
Authors: Lemos Brenda R. , Kaplan Adam C. , Bae Ji Eun , Ferrazzoli Alexander E. , Kuo James , Anand Ranjith P. , Waterman David P. , Haber James E. 
Published: February 2018

Significance
Using budding yeast, we address how Cas9 protein and its guide RNA (gRNA) create double-strand chromosome breaks (DSBs), and explore whether binding of Cas9::gRNA influences subsequent DSB repair by nonhomologous end-joining. We created pairs of gRNAs that are complementary to opposite DNA strands but direct cleavage at the same chromosomal location. The resulting repair profiles (insertion/deletions) are different for the two ostensibly identical DSBs. Most notably, there are frequent +1 insertions that are templated after cleavage creates a 1-nt 5′ overhang that is filled in before ends are ligated. DNA polymerase 4 is required for most +1 insertions and for longer (+2 and +3) insertions. We found similar templating of +1 insertions in published studies of mammalian DSBs created by Cas9.
Piezo2 channel regulates RhoA and actin cytoskeleton to promote cell mechanobiological responses
Authors: Pardo-Pastor Carlos , Rubio-Moscardo Fanny , Vogel-González Marina , Serra Selma A. , Afthinos Alexandros , Mrkonjic Sanela , Destaing Olivier , Abenza Juan F. , Fernández-Fernández José M. , Trepat Xavier , Albiges-Rizo Corinne , Konstantopoulos Konstantinos , Valverde Miguel A. 
Published: February 2018

Significance
The actin cytoskeleton is central to many cellular processes involving changes in cell shape, migration, and adhesiveness. Therefore, there is a great interest in the identification of the signaling pathways leading to the regulation of actin polymerization and assembly into stress fibers (SFs). However, to date it is not well understood how the mechanical interactions between cells and their environment activate the assembly of SFs. Here, we demonstrate that the mechanosensitive Piezo2 channel is required to sense physical cues from the environment to generate a calcium signal that maintains RhoA active and the formation and orientation of SFs and focal adhesions. Besides, this Piezo2-initiated signaling pathway has implications for different hallmarks of cancer invasion and metastasis.
Liprin-α3 controls vesicle docking and exocytosis at the active zone of hippocampal synapses
Authors: Wong Man Yan , Liu Changliang , Wang Shan Shan H. , Roquas Aram C. F. , Fowler Stephen C. , Kaeser Pascal S. 
Published: February 2018

Significance
The presynaptic active zone is important for precise and fast information transfer at central nervous synapses. Invertebrate studies have indicated that Liprin-α proteins are important for active zone assembly and function, but localization and function of vertebrate Liprin-α proteins have remained enigmatic, and pre- or postsynaptic localization and roles have been proposed. Here we used stimulated emission depletion microscopy to directly show that Liprin-α3, but not Liprin-α2, prominently localizes to the active zone. We then generated Liprin-α3–KO mice and found that active zone structure and synaptic vesicle docking and exocytosis are impaired at their synapses. These data establish important functions of Liprin-α3 at the active zone of vertebrate synapses.
High-order above-threshold dissociation of molecules
Authors: Lu Peifen , Wang Junping , Li Hui , Lin Kang , Gong Xiaochun , Song Qiying , Ji Qinying , Zhang Wenbin , Ma Junyang , Li Hanxiao , Zeng Heping , He Feng , Wu Jian 
Published: February 2018

Significance
Above-threshold ionization of atoms in strong laser fields is extensively studied for its overwhelming importance and universality. However, its counterpart, above-threshold dissociation of molecules in strong laser fields, is hard to be observed, although it has been predicted for decades. In this paper, by measuring the momenta of photoelectron and dissociative fragments coincidently, we successfully obtained distinct nuclear energy peaks of the high-order above-threshold dissociation, which must appear simultaneously with the above-threshold ionization. The coexistence of high-order above-threshold dissociation and high-order above-threshold ionization in molecular dissociative ionization offers a perspective to disentangle the complex electron–nuclear correlation in molecules and to image the molecular orbitals, and so on.
Targeting the cMET pathway augments radiation response without adverse effect on hearing in NF2 schwannoma models
Authors: Zhao Yingchao , Liu Pinan , Zhang Na , Chen Jie , Landegger Lukas D. , Wu Limeng , Zhao Fu , Zhao Yanxia , Zhang Yanling , Zhang Jing , Fujita Takeshi , Stemmer-Rachamimov Anat , Ferraro Gino B. , Liu Hao , Muzikansky Alona , Plotkin Scott R. , Stankovic Konstantina M. , Jain Rakesh K. , Xu Lei 
Published: February 2018

Significance
In patients with progressive vestibular schwannoma (VS), radiotherapy is associated with the risk of debilitating hearing loss. There is an urgent need to identify an adjunct therapy that, by enhancing the efficacy of radiation, can help lower the radiation dose and preserve hearing. In our newly developed cerebellopontine angle model of schwannomas that faithfully recapitulates the tumor-induced hearing loss, we demonstrate that cMET blockade sensitizes schwannomas to radiation therapy (RT) in neurofibromatosis type II schwannoma animal models without any adverse effects on hearing. Using an organoid brain slice culture model, cMET blockade inhibited the growth of patient-derived schwannomas. Our study provides the rationale and critical data for the clinical translation of combined cMET blockade with RT in patients with VSs.
Role of ubiquitylation of components of mitotic checkpoint complex in their dissociation from anaphase-promoting complex/cyclosome
Authors: Sitry-Shevah Danielle , Kaisari Sharon , Teichner Adar , Miniowitz-Shemtov Shirly , Hershko Avram 
Published: February 2018

Significance
The mitotic checkpoint system is important for ensuring the correct segregation of chromosomes in mitosis. When chromosomes are not attached correctly to the mitotic spindle, a mitotic checkpoint complex (MCC) is formed that prevents chromosome separation by inhibiting the action of the anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase. MCC is disassembled when the checkpoint is turned off. The disassembly of APC/C-bound MCC was known to require ubiquitylation, but the mechanisms of this process remained unknown. Here we show that two different components of MCC may be ubiquitylated and suggest that these ubiquitylation events lead to their dissociation from each other and from APC/C. Thus, this investigation provides insight into the molecular events responsible for the inactivation of the mitotic checkpoint.
Pivotal roles of PCNA loading and unloading in heterochromatin function
Authors: Janke Ryan , King Grant A. , Kupiec Martin , Rine Jasper 
Published: February 2018

Significance
DNA replication poses a unique logistical challenge for cells in that structural features of chromatin and their regulatory functions must be carefully coordinated with the passage of replication machinery so faithful duplication of both the genome and its chromatin structures may be achieved. Nucleosome assembly is fundamental to reestablishment of chromatin in the wake of DNA replication. Here, a mechanism for coordinating nucleosome assembly with DNA replication to maintain silenced chromatin is described.
Assembly of the membrane domain of ATP synthase in human mitochondria
Authors: He Jiuya , Ford Holly C. , Carroll Joe , Douglas Corsten , Gonzales Evvia , Ding Shujing , Fearnley Ian M. , Walker John E. 
Published: February 2018

Significance
Mitochondria generate the cellular fuel ATP to sustain complex life. Production of ATP depends on the oxidation of energy-rich compounds to produce the proton motive force (pmf), a chemical potential difference for protons, across the inner membrane. The pmf drives the ATP synthase, a molecular machine with a rotary action, to synthesize ATP. We have shown that the assembly of human ATP synthase in the inner organellar membrane involves the formation of a monomeric intermediate made from 25 nuclear-encoded proteins into which the two mitochondrially encoded subunits are inserted and then sealed by association of another nuclear-encoded protein, thereby dimerizing the complex. Association of a final nuclear protein oligomerizes the dimers back-to-face along the cristae edges.
Reporter–nanobody fusions (RANbodies) as versatile, small, sensitive immunohistochemical reagents
Authors: Yamagata Masahito , Sanes Joshua R. 
Published: February 2018

SignificanceConventional antibodies are often poorly defined, limited in amount, and difficult to store permanently. Nanobodies, recombinant antigen-binding proteins derived from single-chain camelid antibodies, circumvent many of these limitations. To maximize the potential of nanobodies, we fused them to highly sensitive reporters and appended sequences to enable ready production and purification. These RANbodies (reporter and nanobody fusions) can be readily produced in cultured cells, purified in a single step, used to label cells or tissue, and stored indefinitely in the form of DNA or DNA sequences. Given the rapidly increasing rate of nanobody generation, the RANbody platform provides a versatile and scalable platform for immunohistochemical and biochemical analyses.
Analysis of politeness strategies in Japanese and Korean conversations between males
Authors: Lee Eun Mi 
Published: February 2018

AbstractThis study analyzed the uses and functions of speech levels and speech level shifts in natural conversations between two unacquainted males. Similarities and differences between Japanese and Korean languages have been investigated. For the Japanese language, speech levels do not clearly reflect the hierarchical relationships based on the interlocutors’ age by utilizing “non-marked utterance (NM)” This finding implies that modern Japanese people tend to avoid the use of honorifics which clearly indicates the hierarchical relationships between speakers at the sentence level. On the other hand, speech level shifts reflect hierarchical relationships between speakers, which means that Japanese seem to conform to normative language use at the discourse level. For the Korean language, both speech levels and speech level shifts clearly reflect the hierarchical relationships based on the interlocutors’ age. This result suggests that Korean have a strong tendency to preserve the normative honorific usage of polite forms according to age difference both at the sentence level and at the discourse level. These results suggest that speech levels, considered to be socio-pragmatically obligatory, have a strategic-use aspect for both languages, including the use of “non-marked utterances” and that of downshifts. It was also discovered that Japanese tend to use speech levels more strategically than Korean. Consequently, Japanese uses honorifics strategically in order to evade hierarchical relationships based on age, whereas Koreans tend to conform to social norms that derive from tenets of Confucianism, a philosophy emphasizing politeness toward older people; such practice encourages younger people to use polite forms to their elders.
An overview of the Japanese quotative itta and itte ita
Authors: Nishi Hironori 
Published: February 2018

Abstract
The present study provides an overview of the quotative utterances made with itta (past form of iu ‘to say’) and itte ita (the combination of iu and the past form of the -te iru construction) in naturally occurring conversations in Japanese. The examination of approximately 13 hours of conversations shows that itta is used in 91.1% of first-person quotations (‘I said that…’). In second-person (‘you said that…’) and third-person (‘he/she said that…’) quotations, itte ita is used in 90.0%, and 77.3% of the cases, respectively. The present study argues that the high percentage of itte ita for second- and third-person quotative utterances is due to the fact that the -te iru construction, which is included in itte ita, is used as an evidential marker. The present study also analyzes the deviant cases from the dominant pattern (i.e. using itta for third-person utterances), and demonstrates how -te iru’s evidential function is utilized manipulatively in conversation.
SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses
Authors: Větrovský Tomáš , Baldrian Petr , Morais Daniel 
Published: February 2018

Abstract

Motivation
Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems.

Results
SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4 GB of data.

Availability and implementation
SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions.

Supplementary information
Supplementary data are available at Bioinformatics online.
Quality of Life After Motor Cortex Stimulation: Clinical Results and Systematic Review of the Literature
Authors: Parravano Daniella C , Ciampi Daniel A , Fonoff Erich T , Monaco Bernardo , Navarro Jessie , Yeng Lin T , Teixeira Manoel J , Hamani Clement 
Published: February 2018

Abstract

BACKGROUND
Motor cortex stimulation (MCS) is routinely used for the treatment of chronic neuropathic pain but its effect on quality of life remains uncertain.

OBEJCTIVE
To systematically review the published literature on MCS and quality of life and report the effects of this therapy in a series of patients prospectively followed in our center.

METHODS
The systematic literature review was conducted using the search words “motor cortex stimulation and pain and neurosurgery” and “motor cortex stimulation and pain and quality of life.” Quality of life in our clinical trial was investigated in a series of 10 patients with chronic neuropathic pain prospectively followed for 12 mo after MCS.

RESULTS
Two hundred eighteen nonreplicated articles were pooled for analysis. Of these, 6 described measures of quality of life in the pre- and postoperative period. In these studies, 64 patients with different clinical conditions associated with neuropathic pain were followed for 6 to 84 mo after MCS surgery. Improvement in quality of life ranged from 35% to 85%.
In our clinical series, visual analog scale (VAS), SF-12 physical (PhysCS), and mental scores (MenCS) recorded 12 mo after MCS were improved by 60 ± 10% (P = .002), 50 ± 13% (P = .002), and 22 ± 6% (P = .01), respectively. No significant correlation was found between postoperative improvement in pain and either PhysCS (r = 0.18; P = .6) or MenCS (r = –0.24; P = .5).

CONCLUSION
MCS improves quality of life in patients with chronic refractory neuropathic pain. Additional factors other than a simple analgesic effect may contribute to these results.
Ulcerated Basal Cell Carcinomas Masquerading as Venous Leg Ulcers
Authors: Tchanque-Fossuo Catherine N. , Millsop Jillian W. , Johnson Mary Ann , Dahle Sara E. , Isseroff R. Rivkah 
Published: February 2018

ABSTRACT

BACKGROUND:
Nonmelanoma skin cancers rarely arise from venous leg ulcers (VLUs). Although basal cell carcinoma (BCC) is the most common nonmelanoma skin cancer, its association with lower-extremity ulcers is not as frequently reported as other malignancies.

OBJECTIVE:
To report a case series of biopsy-proven BCC from lower-extremity ulcers of patients who presented at a multispecialty wound clinic.

METHODS:
Four male patients (mean age, 82.75 years) with 4 chronic VLUs (duration ranging from 2 months to 10 years) underwent a biopsy of their ulcerative lesions.

RESULTS:
Histologic examination of the specimens revealed 4 cases of BCC. All of the lesions were surgically excised, followed by split-thickness skin graft (n = 2) or healing by secondary intention (n = 2). All of the patients remained healed at follow-up ranging from 15 to 27 months, except for 1 patient who opted for conservative management and had not completely healed at 14 months’ follow-up.

CONCLUSIONS:
Biopsies are warranted for any VLU with documented stalled healing following 3 months of standard of care. One biopsy is performed at the periphery of the ulcer and another at the base in order to rule out the presence of malignant transformation because of BCC, squamous cell carcinoma, sarcoma, melanoma, lymphoma, or metastases.