bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagen II Is Essential for the Removal of the Notochord and the Formation of Intervertebral Discs
Authors: Aszódi Attila , Chan Danny , Hunziker Ernst , Bateman John F. , Fässler Reinhard 
Published: July 2002

Collagen II is a fibril-forming collagen that is mainly expressed in cartilage. Collagen II–deficient mice produce structurally abnormal cartilage that lacks growth plates in long bones, and as a result these mice develop a skeleton without endochondral bone formation. Here, we report that Col2a1-null mice are unable to dismantle the notochord. This defect is associated with the inability to develop intervertebral discs (IVDs). During normal embryogenesis, the nucleus pulposus of future IVDs forms from regional expansion of the notochord, which is simultaneously dismantled in the region of the developing vertebral bodies. However, in Col2a1-null mice, the notochord is not removed in the vertebral bodies and persists as a rod-like structure until birth. It has been suggested that this regional notochordal degeneration results from changes in cell death and proliferation. Our experiments with wild-type mice showed that differential proliferation and apoptosis play no role in notochordal reorganization. An alternative hypothesis is that the cartilage matrix exerts mechanical forces that induce notochord removal. Several of our findings support this hypothesis. Immunohistological analyses, in situ hybridization, and biochemical analyses demonstrate that collagens I and III are ectopically expressed in Col2a1-null cartilage. Assembly of the abnormal collagens into a mature insoluble matrix is retarded and collagen fibrils are sparse, disorganized, and irregular. We propose that this disorganized abnormal cartilage collagen matrix is structurally weakened and is unable to constrain proteoglycan-induced osmotic swelling pressure. The accumulation of fluid leads to tissue enlargement and a reduction in the internal swelling pressure. These changes may be responsible for the abnormal notochord removal in Col2a1-null mice.
Our studies also show that chondrocytes do not need a collagen II environment to express cartilage-specific matrix components and to hypertrophy. Furthermore, biochemical analysis of collagen XI in mutant cartilage showed that α1(XI) and α2 (XI) chains form unstable collagen XI molecules, demonstrating that the α3(XI) chain, which is an alternative, posttranslationally modified form of the Col2a1 gene, is essential for assembly and stability of triple helical collagen XI.
Searching DNA databases for similarities to DNA sequences: when is a match significant?
Authors: Anderson I , Brass A 
Published: July 2002

Abstract
MOTIVATION: Searching DNA sequences against a DNA database is an essential element of sequence analysis. However, few systematic studies have been carried out to determine when a match between two DNA sequences has biological significance and this is limiting the use that can be made of DNA searching algorithms. RESULTS: A test set of DNA sequences has been constructed consisting of artificially evolved and real sequences. This set has been used to test various database searching algorithms (BLAST, BLAST2, FASTA and Smith-Waterman) on a subset of the EMBL database. The results of this analysis have been used to determine the sensitivity and coverage of all of the algorithms. Guidelines have been produced which can be used to assess the significance of DNA database search results. The Smith-Waterman algorithm was shown to have the best coverage, but the worst sensitivity, whereas the default BLASTN algorithm (word length set to 11) was shown to have good sensitivity, but poor coverage. A sensible compromise between speed, sensitivity and coverage can be obtained using either the FASTA or BLAST (word length set to 6) algorithms. However, analysis of the results also showed that no algorithm works well when the length of the probe sequence is &lt;200 bases. In general, matches can accurately be identified between coding regions of DNA sequences when there is &gt;35% sequence identity between the corresponding proteins. Searching a DNA sequence against a DNA sequence database can, therefore, be a useful tool in sequence analysis. AVAILABILITY: The test sets used are available via anonymous ftp from mbisg2.sbc.man.ac.uk in the directory /pub/cabios/testdata/ CONTACT: I.Anderson@stud.man.ac.uk; abrass@man.ac.uk
A neural network classifier capable of recognizing the patterns
of all major subcellular structures in fluorescence microscope
images of HeLa cells
Authors: Boland Michael V. , Murphy Robert F. 
Published: July 2002

Abstract
Motivation: Assessment of protein subcellular location is crucial to proteomics efforts since localization information provides a context for a protein’s sequence, structure, and function. The work described below is the first to address the subcellular localization of proteins in a quantitative, comprehensive manner.
Results: Images for ten different subcellular patterns (including all major organelles) were collected using fluorescence microscopy. The patterns were described using a variety of numeric features, including Zernike moments, Haralick texture features, and a set of new features developed specifically for this purpose. To test the usefulness of these features, they were used to train a neural network classifier. The classifier was able to correctly recognize an average of 83% of previously unseen cells showing one of the ten patterns. The same classifier was then used to recognize previously unseen sets of homogeneously prepared cells with 98% accuracy.
Availability: Algorithms were implemented using the commercial products Matlab, S-Plus, and SAS, as well as some functions written in C. The scripts and source code generated for this work are available at http://murphylab.web.cmu.edu/software.
Contact: murphy@cmu.edu
* To whom correspondence should be addressed.
Nanosized Fat Emulsion Injection Modulating Local Microenvironment Promotes Angiogenesis in Chronic Wound Healing
Authors: Xian Caihong , Zhang Zhen , You Xinru , Fang Yifen , Wu Jun 
Published: May 2022

AbstractThe current treatment for chronic diabetic wounds is costly for patients and society. The proinflammatory state and impaired vascular condition are the main factors that hamper diabetic wound healing. In this study, fat emulsion (FE), a nanosized product clinically used to provide nutrition and energy to patients through vein injection, is evaluated for its diabetic wound healing capability for the first time. The nanosized FE is mixed with methacrylated hyaluronic acid (HA–MA) hydrogel to form an anti‐inflammatory and angiogenic FE/HA–MA hybrid hydrogel dressing to accelerate the diabetic wound closure. Results of RT‐qPCR analysis and ELISA demonstrate that the FE exerts excellent anti‐inflammatory effects by significantly downregulating the expression of proinflammatory cytokines tumor necrosis factor‐α (TNF‐α) and interleukin‐1β (IL‐1β), both in vitro and in vivo. The endothelial tube formation and scratch assays reveal that the FE promotes angiogenesis and cell migration, respectively, by releasing vascular endothelial growth factor A. The in vivo diabetic wound mouse model confirms an increased blood vessel density, healing rate, tissue epithelialization, and collagen deposition in the FE/HA–MA hybrid hydrogel dressing group compared to the control group. These findings may provide a promising and economic product and strategy for diabetic wound treatment in the clinic.
Initial guess estimation and fast solving of petroleum complex molecular reconstruction model
Authors: Guan Dong , Zhang Linzhou 
Published: May 2022

AbstractWe proposed a fast method to solve the petroleum molecular reconstruction problem via initial guess estimation coupled with local optimization algorithm. A virtual oil database was constructed. After inputting the bulk properties of the target oil, several virtual oils with similar bulk properties were selected and their model parameters were used as the initial guesses. Subsequently, we proved that by using a local optimization method, the optimal model parameters can be rapidly obtained. The diesel and vacuum gas oil compositional models were exemplified as case studies. The results show that the proposed method presented faster computational time, which is within the range of 20–50 times that of frequently used global algorithms. Moreover, the optimal solution of the proposed method exhibited higher accuracy. In addition, the effect of the number of virtual oils and the parallel computation performance were also investigated.
Undiagnosed disease program in South Africa: Results from first 100 exomes
Authors: Moosa Shahida , Coetzer Kimberly Christine , Lee Eugene , Seo Go Hun 
Published: May 2022

AbstractThe Undiagnosed Disease Program in South Africa (UDP) sought to prospectively evaluate the clinical utility of exome sequencing (ES) in a phenotypically diverse, multi‐ethnic cohort of South African patients with suspected rare genetic disorders. ES was undertaken in 100 sequential patients (93 singletons, 3 duos, and 4 trios) recruited to the UDP at Stellenbosch University. The data were analyzed through two separate bioinformatics pipelines (EVIDENCE from 3 billion and our in‐house pipeline). A definitive diagnosis could be reached in 51% (51/100) patients, with 46% (46/100) patients having either pathogenic or likely pathogenic single‐nucleotide variants/indels (SNVs/indels), and 5 patients with likely‐pathogenic copy number variants (CNVs) (5/100). The CNVs were subsequently confirmed on microarray or MLPA analysis. Detailed phenotyping and HPO terms enabled analysis and variant identification. Twenty‐five novel variants in 22 genes are reported here. We provide data from the first year of this UDP and show that even amongst mainly singletons from an understudied, diverse African population, ES is a valuable diagnostic tool, especially if it includes CNV analysis. The remaining undiagnosed patients present a unique opportunity for further research and novel gene discovery.
Integrative Approach to Predict Severity in Nonketotic Hyperglycinemia
Authors: Kuseyri Hübschmann Oya , Juliá‐Palacios Natalia Alexandra , Olivella Mireia , Guder Philipp , Zafeiriou Dimitrios I. , Horvath Gabriella , Kulhánek Jan , Pearson Toni S. , Kuster Alice , Cortès‐Saladelafont Elisenda , Ibáñez Salvador , García‐Jiménez Maria Concepción , Honzík Tomáš , Santer René , Jeltsch Kathrin , Garbade Sven F. , Hoffmann Georg F. , Opladen Thomas , García‐Cazorla Ángeles 
Published: May 2022

ObjectiveGlycine encephalopathy, also known as nonketotic hyperglycinemia (NKH), is an inherited neurometabolic disorder with variable clinical course and severity, ranging from infantile epileptic encephalopathy to psychiatric disorders. A precise phenotypic characterization and an evaluation of predictive approaches are needed.MethodsLongitudinal clinical and biochemical data of 25 individuals with NKH from the patient registry of the International Working Group on Neurotransmitter Related Disorders were studied with in silico analyses, pathogenicity scores, and molecular modeling of GLDC and AMT variants.ResultsSymptom onset (p < 0.01) and diagnosis occur earlier in life in severe NKH (p < 0.01). Presenting symptoms affect the age at diagnosis. Psychiatric problems occur predominantly in attenuated NKH. Onset age ≥ 3 months (66% specificity, 100% sensitivity, area under the curve [AUC] = 0.87) and cerebrospinal fluid (CSF)/plasma glycine ratio ≤ 0.09 (57% specificity, 100% sensitivity, AUC = 0.88) are sensitive indicators for attenuated NKH, whereas CSF glycine concentration ≥ 116.5μmol/l (100% specificity, 93% sensitivity, AUC = 0.97) and CSF/plasma glycine ratio ≥ 0.15 (100% specificity, 64% sensitivity, AUC = 0.88) are specific for severe forms. A ratio threshold of 0.128 discriminates the overlapping range. We present 10 new GLDC variants. Two mild variants resulted in attenuated, whereas 2 severe variants or 1 mild and 1 severe variant led to severe phenotype. Based on clinical, biochemical, and genetic parameters, we propose a severity prediction model.InterpretationThis study widens the phenotypic spectrum of attenuated NKH and expands the number of pathogenic variants. The multiparametric approach provides a promising tool to predict disease severity, helping to improve clinical management strategies. ANN NEUROL 2022;92:292–303
Clinical Issues—June 2022
Authors: Jones Emily 
Published: May 2022

THIS MONTH
Electrostatic precipitator device use during laparoscopic surgery
Key words: electrostatic precipitation (ESP), surgical smoke precipitator, anions, visual field, medical device reporting (MDR).
Removal of used flammable skin antisepsis materials
Key words: flammable liquid antiseptics, National Fire Protection Association (NFPA), fire prevention, fire risk, patient care vicinity.
Ocular protection for patients with eyelash extensions
Key words: ocular injury, eyelash extensions, eye protection, lagophthalmos, intraocular pressure.
Perioperative nursing care of the patient with Raynaud’s phenomenon
Key words: ischemia, vasospasm, comfort measures, hypothermia, complementary care.
Conductive polycarbonate composites prepared by a ternary polymer blend approach involving sea‐island‐type interfacial carbon black networks
Authors: Li Hansong , Tuo Xinlin , Xing Ziyi , Guo Bao‐Hua , Yu Jian , Guo Zhao‐Xia 
Published: May 2022

AbstractTernary blends containing one major and two minor components are a common type of polymer blends, however, they have never been used to improve the electrical conductivity of polymer composites. Herein, polycarbonate (PC)/nylon‐poly(m‐xylene adipamide) (MXD6)/poly(ethylene terephthalate) (PET) (70/15/15) ternary blend is used to improve the conductivity of PC by forming sea‐island type interfacial carbon black (CB) networks. The phase change of PET from island to continuous structure, caused by the formation of CB networks at PET/MXD6 interface, is the key of success. The electrical percolation threshold of CB is much smaller than that in neat PC (only a ninth). Rheological investigation is carried out to confirm the formation of CB networks. The static mechanical properties of PC/MXD6/PET (70/15/15)‐2 vol% CB composite are evaluated by tensile testing, showing improved stiffness and strength, compared with the corresponding ternary blend, neat PC, and PC‐2 vol% CB composite.
Cover Image, Volume 16, Issue 3
Authors: Phillips Steven D. , Jones Susanne B. , Meyer Pimphan A. , Snowden‐Swan Lesley J. 
Published: May 2022

AbstractThe cover image is based on the Research Article Techno‐economic analysis of cellulosic ethanol conversion to fuel and chemicals by Steven Phillips et al., https://doi.org/10.1002/bbb.2346.
image
Einsatz von Hydrophobierungen nach der TR Instandhaltung des DIBt – Vorgehen aus der Perspektive des Planers und Praxisbeispiel
Authors: Schießl‐Pecka Angelika , Strehlein Doris 
Published: May 2022

AbstractNach der Technischen Regel Instandhaltung (TR IH) des Deutschen Instituts für Bautechnik (DIBt) [1], die bereits in einigen Bundesländern bauaufsichtlich eingeführt ist, ist im Gegensatz zum Teil 1 der Instandsetzungsrichtlinie des DAfStb [2] auch die Verwendung von Hydrophobierungen bzw. OS1‐Systemen zum Schutz gegen das Eindringen von Stoffen, zur Regulierung des Wasserhaushalts von Beton und zur Erhöhung des elektrolytischen Widerstands von Beton (bei carbonatisierungsinduzierter Bewehrungskorrosion) möglich. Im vorliegenden Beitrag wird ein Überblick über die am Markt erhältlichen Produktgruppen an Hydrophobierungen auf Silan‐ oder Siloxan‐Basis gegeben. Da der Planer nach der TR IH Auftragsmengen und Eindringtiefen vorgeben muss, werden das Vorgehen zur Bestimmung von Mindestauftragsmengen und Mindesteindringtiefen skizziert und entsprechende Laborprüfungen zur Bestimmung der Mindestwerte vorgestellt. Weiterhin werden Hinweise zur Planung und Qualitätssicherung während der Bauausführung gegeben. Eine während der Nutzung möglicherweise nachlassende Wirkung einer Hydrophobierung muss gemäß TR IH durch Kontrollmessungen im Instandhaltungsplan berücksichtigt werden. In diesem Zusammenhang werden verschiedene Möglichkeiten erläutert, mit denen ein solcher Wirkungsnachweis möglich ist. Abschließend wird ein Praxisbeispiel vorgestellt.
Characterizing biological macromolecules with attenuated total reflectance–Fourier transform infrared spectroscopy provides hands‐on spectroscopy experiences for undergraduates
Authors: Helburn Robin , Nolan Kathleen 
Published: May 2022

AbstractInfrared (IR) spectra of biologically derived materials display distinct absorption bands correlating to individual macromolecules: protein, polysaccharide, lipid, and nucleic acids. A series of experiments aimed at teaching qualitative bioorganic spectroscopy using attenuated total reflectance (ATR) Fourier transform infrared (IR) with biological polymers as samples is proposed. Labs targeting 1st and 4th year undergraduate students at St. Francis College are being developed. During 2014 ➔ 2017, an integrated biology/chemistry exercise featuring elementary spectroscopy as an addition to an existing lab on light microscopy was administered to three sections of a 1st year general biology course. Students were taught the concept of a spectral fingerprint and to identify carbohydrate and protein based materials by looking for key vibrational bands. The success of that effort as determined by the results of an assessment quiz became the motivation for developing an advanced 4th year exercise involving four macromolecules. In a trial lab (Spring 2019) students gathered reference spectra from materials homogeneous in a single biopolymer followed by spectra of whole tissues which they were expected to fully characterize. Assessment data suggest that 1st year students benefited most from the experience. A detailed discussion of reference and sample spectra (as obtained by students) and relevant bond vibrations along with suggestions for instructors are presented.
The Milan System classification of Warthin tumor: A large institutional study of 124 cases highlighting cytologic features that limit definitive interpretation
Authors: Torous Vanda F. , Faquin William C. 
Published: May 2022

BACKGROUNDFine‐needle aspiration (FNA) is highly accurate for the diagnosis of Warthin tumor (WT). However, there is a minor subset of WT cases that are more challenging to interpret. The goal of this study is to identify factors that limit definitive diagnosis of WT on FNA.METHODSAll WT surgical specimens diagnosed during a 6.5‐year study period were retrospectively identified and the preceding cytologic specimen diagnostic categories were analyzed. Of particular interest were WT cases with indeterminate or malignant interpretations. Cases that noted squamous or mucinous change in either the surgical or cytologic reports were also reviewed.RESULTSA total of 157 WT surgical specimens were identified, with 124 (79.0%) having prior FNAs. The distribution of cytologic diagnostic categories was 12 (9.7%) nondiagnostic, 10 (8.1%) nonneoplastic, 13 (10.5%) atypia of undetermined significance (AUS), 82 (66.1%) neoplasm: benign, 4 (3.2%) salivary gland neoplasm of uncertain malignant potential (SUMP), 2 (1.6%) suspicious for malignancy, and 1 (0.8%) malignant. Of the 20 cases in indeterminate/malignant categories, a majority noted either squamoid (9 of 20) or mucinous (2 of 20) changes. The remainder noted scant cellularity as a limiting factor to interpretation. Additionally, 27 cases mentioned squamous or mucinous change in the surgical or cytology report, with a wide spectrum of cytologic categorization including 2 (7.4%) nondiagnostic, 2 (7.4%) nonneoplastic, 7 (25.9%) AUS, 8 (29.6%) neoplasm: benign, 4 (14.8%) SUMP, 2 (7.4%) suspicious for malignancy, and 1 (3.7%) malignant.CONCLUSIONSThis study identified 2 key causes for indeterminate or misclassification of WT on FNA: specimen hypocellularity and metaplastic changes. Recognition of the potential for squamous and mucinous metaplastic changes combined with observance of some helpful diagnostic clues such as the presence of crystalloids may aid in preventing diagnostic pitfalls.;
Cognitive Long‐range: Towards efficient public communication infrastructure for Internet of Things
Authors: Mousavi Seyed Mehdi , Khademzadeh Ahmad , Rahmani Amir Masoud 
Published: May 2022

SummaryThe most common Internet of Things (IoT) scenarios entail devices with limited energy resources and need to be connected to the Internet via wireless networks. This has driven the recent development of low‐power wide‐area networks (LPWANs) and the rise of the Long Range (LoRa) technology. The LoRa protocol has a simple modulation scheme that ensures low power consumption, high convergence, and resistance against interference. In most LPWAN technologies, several physical layer challenges arise, such as low data rates, spectral inefficiency, and increased interference. As a physical layer solution, the cognitive radio (CR) offers a possible way of resolving these challenges. CR allows wireless networks to operate without the need for a dedicated spectrum. Regarding the variety of end‐user requirements, developing a public communication network that can support such diverse and heterogeneous applications is necessary to reduce the implementation costs than developing a dedicated communication network for each application. This paper proposes a Cognitive LoRa (C‐LoRa) protocol that utilizes unlicensed and licensed frequencies as well as interference mitigation to improve the QoS of LoRa. To extract the priority list of traffic patterns, C‐LoRa incorporates the Analytic Hierarchy Process (AHP) algorithm. The priority list enables real‐time applications to receive optimal spectrum allocation. C‐LoRa can be efficiently implemented as a public communication infrastructure for heterogeneous IoT devices. The addition of licensed channels improves the overall QoS and decreases the average waiting time in queues. The platform layer of C‐LoRa consists of a cognitive engine that sends traffic priority lists to cognitive spectrum allocators. The IoT application servers are connected to the cloud platform layer via SNMP, HTTP, and other desired protocols. Access gateways equipped with a cognitive spectrum allocator are always connected to a power supply and serve as a transparent bridge to the cognitive engine at the platform layer, converting RF packets to IP packets and vice versa.
A comprehensive analytical perspective of ASEP for Beaulieu‐Xie fading channels
Authors: Bilim Mehmet 
Published: May 2022

SummaryThis study presents the average symbol error probability (ASEP) performance of a single‐input single‐output communication with imperfect phase error (IPE) and without IPE over the Beaulieu‐Xie fading channels. The Beaulieu‐Xie fading model is proposed recently and it is a popular characterization for the line‐of‐sight and non‐line‐of‐sight environments. The proposed theoretical analysis, which is based on the probability density function, is enough general and applicable in some real‐life scenarios. For both cases, closed‐form exact, approximate, and asymptotic expressions are derived for the ASEP of different modulation types. Finally, exact simulations have been introduced to confirm the accuracy of the theoretical findings obtained and present insights into the considered scheme performance.