bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial organization of active and inactive genes and noncoding DNA within chromosome territories
Authors: Mahy Nicola L. , Perry Paul E. , Gilchrist Susan , Baldock Richard A. , Bickmore Wendy A. 
Published: July 2002

The position of genes within the nucleus has been correlated with their transcriptional activity. The interchromosome domain model of nuclear organization suggests that genes preferentially locate at the surface of chromosome territories. Conversely, high resolution analysis of chromatin fibers suggests that chromosome territories do not present accessibility barriers to transcription machinery.
To clarify the relationship between the organization of chromosome territories and gene expression, we have used fluorescence in situ hybridization to analyze the spatial organization of a contiguous ∼1 Mb stretch of the Wilms' tumor, aniridia, genitourinary anomalies, mental retardation syndrome region of the human genome and the syntenic region in the mouse. These regions contain constitutively expressed genes, genes with tissue-restricted patterns of expression, and substantial regions of intergenic DNA. We find that there is a spatial organization within territories that is conserved between mouse and humans: certain sequences do preferentially locate at the periphery of the chromosome territories in both species. However, we do not detect genes necessarily at the periphery of chromosome territories or at the surface of subchromosomal domains. Intraterritory organization is not different among cell types that express different combinations of the genes under study.
Our data demonstrate that transcription of both ubiquitous and tissue-restricted genes is not confined to the periphery of chromosome territories, suggesting that the basal transcription machinery and transcription factors can readily gain access to the chromosome interior.
Characterizations of spectra with 𝒰-injective cohomology which satisfy the Brown-Gitler property
Authors: Hunter David , Kuhn Nicholas 
Published: July 2002

We work in the stable homotopy category of

p
p

–complete connective spectra having mod

p
p

homology of finite type.

H
∗

(
X
)

H^*(X)

means cohomology with

Z

/

p

\mathbf {Z}/p

coefficients, and is a left module over the Steenrod algebra

A

\mathcal {A}

. A spectrum

Z
Z

is called spacelike if it is a wedge summand of a suspension spectrum, and a spectrum

X
X

satisfies the Brown–Gitler property if the natural map

[
X
,
Z
]
→

Hom

A

⁡
(

H
∗

(
Z
)
,

H
∗

(
X
)
)

[X,Z] \rightarrow \operatorname {Hom}_{\mathcal {A}}(H^*(Z),H^*(X))

is onto, for all spacelike

Z
Z

. It is known that there exist spectra

T
(
n
)

T(n)

satisfying the Brown–Gitler property, and with

H
∗

(
T
(
n
)
)

H^*(T(n))

isomorphic to the injective envelope of

H
∗

(

S
n

)

H^*(S^n)

in the category

U

\mathcal {U}

of unstable

A

\mathcal {A}

–modules. Call a spectrum

X
X

standard if it is a wedge of spectra of the form

L
∧
T
(
n
)

L \wedge T(n)

, where

L
L

is a stable wedge summand of the classifying space of some elementary abelian

p
p

–group. Such spectra have

U

\mathcal {U}

–injective cohomology, and all

U

\mathcal {U}

–injectives appear in this way. Working directly with the two properties of

T
(
n
)

T(n)

stated above, we clarify and extend earlier work by many people on Brown–Gitler spectra. Our main theorem is that, if

X
X

is a spectrum with

U

\mathcal {U}

–injective cohomology, the following conditions are equivalent: (A) there exist a spectrum

Y
Y

whose cohomology is a reduced

U

\mathcal {U}

–injective and a map

X
→
Y

X \rightarrow Y

that is epic in cohomology, (B) there exist a spacelike spectrum

Z
Z

and a map

X
→
Z

X \rightarrow Z

that is epic in cohomology, (C)

ϵ
:

Σ

∞

Ω

∞

X
→
X

\epsilon :\Sigma ^{\infty }\Omega ^{\infty }X \rightarrow X

is monic in cohomology, (D)

X
X

satisfies the Brown–Gitler property, (E)

X
X

is spacelike, (F)

X
X

is standard. (

M
∈

U

M \in \mathcal {U}

is reduced if it has no nontrivial submodule which is a suspension.) As an application, we prove that the Snaith summands of

Ω
2

S
3

\Omega ^2S^3

are Brown–Gitler spectra–a new result for the most interesting summands at odd primes. Another application combines the theorem with the second author’s work on the Whitehead conjecture. Of independent interest, enroute to proving that (B) implies (C), we prove that the homology suspension has the following property: if an

n
n

–connected space

X
X

admits a map to an

n
n

–fold suspension that is monic in mod

p
p

homology, then

ϵ
:

Σ
n

Ω
n

X
→
X

\epsilon : \Sigma ^n\Omega ^n X \rightarrow X

is onto in mod

p
p

homology.
Compactly supported tight affine spline frames in 𝐿₂(ℝ^{𝕕})
Authors: Ron Amos , Shen Zuowei 
Published: July 2002

The theory of fiberization is applied to yield compactly supported tight affine frames (wavelets) in

L

2

(

R

d

)

L_{2}(\mathbb {R}^{d})

from box splines. The wavelets obtained are smooth piecewise-polynomials on a simple mesh; furthermore, they exhibit a wealth of symmetries, and have a relatively small support. The number of “mother wavelets”, however, increases with the increase of the required smoothness. Two bivariate constructions, of potential practical value, are highlighted. In both, the wavelets are derived from four-direction mesh box splines that are refinable with respect to the dilation matrix

(

1

a
m
p
;
1

1

a
m
p
;
−
1

)

\begin {pmatrix}1&1\ 1&-1\end {pmatrix}

.
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Authors: Andrade M A , Valencia A 
Published: July 2002

Abstract
MOTIVATION: Annotation of the biological function of different protein sequences is a time-consuming process currently performed by human experts. Genome analysis tools encounter great difficulty in performing this task. Database curators, developers of genome analysis tools and biologists in general could benefit from access to tools able to suggest functional annotations and facilitate access to functional information. APPROACH: We present here the first prototype of a system for the automatic annotation of protein function. The system is triggered by collections of s related to a given protein, and it is able to extract biological information directly from scientific literature, i.e. MEDLINE abstracts. Relevant keywords are selected by their relative accumulation in comparison with a domain-specific background distribution. Simultaneously, the most representative sentences and MEDLINE abstracts are selected and presented to the end-user. Evolutionary information is considered as a predominant characteristic in the domain of protein function. Our system consequently extracts domain-specific information from the analysis of a set of protein families. RESULTS: The system has been tested with different protein families, of which three examples are discussed in detail here: 'ataxia-telangiectasia associated protein', 'ran GTPase' and 'carbonic anhydrase'. We found generally good correlation between the amount of information provided to the system and the quality of the annotations. Finally, the current limitations and future developments of the system are discussed. AVAILABILITY: The current system can be considered as a prototype system. As such, it can be accessed as a server at http://columba.ebi.ac. uk:8765/andrade/abx. The system accepts text related to the protein or proteins to be evaluated (optimally, the result of a MEDLINE search by keyword) and the results are returned in the form of Web pages for keywords, sentences and s. SUPPLEMENTARY INFORMATION: Web pages containing full information on the examples mentioned in the text are available at: http://www.cnb.uam.es/ approximately cnbprot/keywords/ CONTACT: valencia@cnb.uam.es
Domain identification by clustering sequence alignments.
Authors: Guan X , Du L 
Published: July 2002

Abstract
MOTIVATION: As sequence databases grow rapidly, results from sequence comparison searches using fast search methods such as BLAST and FASTA tend to be long and difficult to digest. RESULTS: In this paper, we present a new method to extract domain information from sequence comparison searches by clustering the resulting alignments according to their similarity to the query sequence. Efficient tree structures and algorithms are used to organize the alignment data such that structurally conserved elements can be easily identified. The hierarchical nature of the data structures used and the flexible X-Window-based interface provide an efficient and intuitive means to explore the alignment data at different levels so that the common domains, as well as distantly related features, can be explored. AVAILABILITY: The clustering program is available by anonymous ftp at: ftp.embl-ebi.ac.uk under directory /pub/software/unix, file: clustering.tar.Z.
Engineering support vector machine kernels that recognize

translation initiation sites
Authors: Zien A. , Rätsch G. , Mika S. , Schölkopf B. , Lengauer T. , Müller K.-R. 
Published: July 2002

Abstract
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS).
Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.
Contact: {Alexander.Zien,Gunnar.Raetsch,Sebastian. Mika}@gmd.de; bsc@microsoft.com
To whom correspondence should be addressed.
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
Authors: Schacherer Frank , Choi Claudia , Götze Ulrike , Krull Mathias , Pistor Susanne , Wingender Edgar 
Published: July 2002

Abstract
TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al. , Nucleic Acids Res. , 28, 316–319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like complexes, signaling molecules, and their states are stored together with information about their interaction in an object-oriented database. The database interface provides clickable maps and automatically generated pathway cascades as additional ways to explore the data. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others).
Availability: The database is available over (http://transpath.gbf.de) for interactive perusal. As an exchange format for the data, eXtensible Markup Language (XML) flatfiles and a Document Type Definition (DTD) are provided.
Contact: frs@biobase.de; cch@biobase.de; ulg@biobase.de; mkl@biobase.de; ewi@biobase.de; spi@biobase.de
Role of the single disulphide bond of β2‐microglobulin in amyloidosis in vitro
Authors: Smith David P. , Radford Sheena E. 
Published: July 2002

AbstractThe aggregation of β2‐microglobulin (β2m) into amyloid fibrils occurs in the condition known as dialysis‐related amyloidosis (DRA). The protein has a β‐sandwich fold typical of the immunoglobulin family, which is stabilized by a highly conserved disulphide bond linking Cys25 and Cys80. Oxidized β2m forms amyloid fibrils rapidly in vitro at acidic pH and high ionic strength. Here we investigate the role of the single disulphide bond of β2m in amyloidosis in vitro. We show that reduction of the disulphide bond destabilizes the native protein such that non‐native molecules are populated at neutral pH. These species are prone to oligomerization but do not form amyloid fibrils when incubated for up to 8 mo at pH 7.0 in 0.4 M NaCl. Over the pH range 4.0–1.5 in the presence of 0.4 M NaCl, however, amyloid fibrils of reduced β2m are formed. These fibrils are ∼10 nm wide, but are shorter and assemble more rapidly than those produced from the oxidized protein. These data show that population of non‐native conformers of β2m at neutral pH by reduction of its single disulphide bond is not sufficient for amyloid formation. Instead, association of one or more specific partially unfolded molecules formed at acid pH are necessary for the formation of β2m amyloid in vitro. Further experiments will now be needed to determine the role of different oligomeric species of β2m in the toxicity of the protein in vivo.
Identification of a region in G protein γ subunits conserved across species but hypervariable among subunit isoforms
Authors: Cook Lana A. , Schey Kevin L. , Cleator John H. , Wilcox Michael D. , Dingus Jane , Hildebrandt John D. 
Published: July 2002

AbstractThe heterotrimeric GTP binding proteins, G proteins, consist of three distinct subunits: α, β, and γ. There are 12 known mammalian γ subunit genes whose products are the smallest and most variable of the G protein subunits. Sequencing of the bovine brain γ10 protein by electrospray mass spectrometry revealed that it differs from the human protein by an Ala to Val substitution near the N‐terminus. Comparison of γ isoform subunit sequences indicated that they vary substantially more at the N‐terminus than at other parts of the protein. Thus, species variation of this region might reflect the lack of conservation of a functionally unimportant part of the protein. Analysis of 38 γ subunit sequences from four different species shows that the N‐terminus of a given γ subunit isoform is as conserved between different species as any other part of the protein, including highly conserved regions. These data suggest that the N‐terminus of γ is a functionally important part of the protein exhibiting substantial isoform‐specific variation.
Effects of increasing internal end‐point temperatures on physicochemical and sensory properties of meat: A review
Authors: Schwartz Marbi , Marais Jeannine , Strydom Phillip Evert , Hoffman Louwrens Christiaan 
Published: April 2022

AbstractAlthough many efforts have been made to improve and control the eating quality of meat, there is still high variability in palatability, which may ultimately result in customer dissatisfaction. Beef meat is especially intricate to study since consumers have specific preferences for degrees of doneness. The degrees of doneness in beef is known to affect its physicochemical properties and have a subsequent effect on palatability. Nevertheless, an in‐depth investigation into the exact changes that occur with increasing internal end‐point temperatures of meat is yet to be explored. With researchers implementing various cooking methods and cooking conditions (i.e., sample preparation and internal end‐point temperatures), the results of studies are often impossible to compare. This review provides an overview of the various benefits and drawbacks of the cooking methods commonly used at home, in commercial enterprises, and research on meat. Furthermore, the physicochemical changes in meat with increasing degrees of doneness are discussed in detail with considerations of the subsequent changes in the sensory properties of meat.
Assessing Seismic Origin of Geological Features by Fitting Equidistant Parallel Lines
Authors: Jupp P.E. , Goudie I.B.J. , Batchelor R.A. , Goudie R.J.B. 
Published: April 2022

AbstractSome planes in sedimentary rocks contain features that appear to lie near equally spaced parallel lines. Determining whether or not they do so can provide information on possible mechanisms for their formation. The problem is recast here in terms of circular statistics, enabling closeness of candidate sets of lines to the points to be measured by a mean resultant length. This leads to a test of goodness of fit and to estimates of the direction of the lines and of the spacing between them. Two contrasting data sets are analysed.
Physical activity and well-being of students of faculties medical and non-medical services during the Covid-19 pandemic
Authors: Sochacka Magdalena , Zdziarski Krzysztof 
Published: April 2022

Physical activity has a positive effect on the human body, well-being and mental health. This is confirmed by the results of studies which show that regular physical exercise has a beneficial effect not only on the cardiovascular, muscular and nervous systems, as well as on mental well-being. The Covid-19 pandemic, which affected society as a whole, changed our lives. The pandemic has a social and economic scope, increasing the number of stressful situations that affect well-being. Aim of the research: The aim of the undertaken research was to check the level of physical activity and well-being of medical and non-medical students during the pandemic. Material and methods: The research used the method of diagnostic survey, with the use of the proprietary questionnaire and the International Physical Activity Questionnaire (IPAQ) as well as a 36-point Health Survey were used. The research group consisted of students of medical and non-medical faculties. Results: The research confirmed a decrease in physical activity and a change in well-being in students of both faculties. The vast majority of students (80%) noticed a change in well-being during the pandemic. Half of the respondents (50%) undertake physical activity to improve their well-being, and over 60% of the students declared that physical activity helps them maintain their well-being during the pandemic. Conclusions: The results of the conducted research indicate a negative impact of the pandemic on the physical activity and well-being of the respondents. There was a strong correlation between physical activity and the well-being of research participants. The greatest decrease in physical activity was observed in medical students (52.08%). On the other hand, students of non-medical faculties (54.17%) showed a lower level of well-being, and higher medical students (45.83%). It is advisable to take preventive measures through active physical activity in order to eliminate the negative effects of the pandemic.
BASF Group as the prominent enterprise in light of the COVID-19 pandemic-overview of the selected financial indicators
Authors: Mrozek Michał 
Published: April 2022

Purpose of the study: The research regards the selected financial indicators: employment, personnel costs, and sales in BASF Group in terms of the COVID-19 pandemic. The paper's fundamental aim is to assess the financial situation of the BASF Group in light of the COVID-19 pandemic from 2016 to 2021.
Methodology: The paper uses statistical, dynamics, comparative, and documentation analysis.
Main findings: The discussion shows that the prominent company within the chemistry sector succeeded in the research period. BASF implemented the suitable mechanisms, solutions, and actions that mitigated the impact of the COVID-19 pandemic and, in consequence, positioned the world pioneer in chemistry in the leading rank against the rest of the entities competing in that diversified market.
Application of the study: The presented paper regards the leading company in the chemistry sector. It focuses on the considerations in such scientific areas as employment, personnel costs, and sales. Applying the instruments and measures of financial analysis enables one to examine the crucial problems of the enterprise. The issues pointed out in the paper can be profitable for practitioners, decision-makers, and managers.
Originality/Novelty of the study: The pandemic's trajectory is challenging to forecast. The COVID-19 pandemic modifications can cause the growth of infected people. Furthermore, the defined financial activity resulting from additional lockdowns may negatively impact aggregate demand. The paper can motivate further study and examination of the financial indicators of the BASF and other inspiring scientific research.
propósito de un caso. Osteogénesis imperfecta tipo III en mujer adulta. Diez años de tratamiento con bifosfonatos. ¿Y ahora qué?
Authors: Pérez-Blanco Carmen , Pavón-de Paz Isabel , Navea-Aguilera Cristina , Rosado-Sierra José Antonio , García-García Diego 
Published: April 2022

La osteogénesis imperfecta (OI) es una enfermedad hereditaria que agrupa defectos del tejido conectivo que causan fragilidad y deformidades óseas. La baja densidad mineral ósea y la alta incidencia de dolor óseo y fracturas obliga a plantear tratamiento dirigido antirresortivo, siendo los bifosfonatos el tratamiento de elección. La eficacia de estos tratamientos está claramente establecida en la infancia, pero no así en la edad adulta. Se presenta el caso de una mujer de 35 años con OI tipo III, que había sido tratada durante diez años con ácido zoledrónico intravenoso. El caso permite revisar los tratamientos empleados hasta la fecha.
Proteinosis alveolar pulmonar en paciente con trombocitemia esencial
Authors: Romero-Francés Laura , Royo-Prats Juan Antonio 
Published: April 2022

La proteinosis alveolar pulmonar es una enfermedad que se caracteriza por la acumulación intraalveolar de componentes del surfactante que provoca deterioro del intercambio gaseoso. Presentamos a un varón de 58 años, con diagnóstico de proteinosis alveolar y antecedente de trombocitemia esencial al que se trató con lavados pulmonares totales, terapia con GM-CSF y rituximab, sin poder frenar el curso de la enfermedad. Revisamos las diversas formas clínicas y líneas de tratamiento.
Trombosis de la arteria hepática. Reporte de un caso clínico y revisión de la literatura
Authors: Lorca-Barchín José , Pascual-Pérez Reyes , Telenti-Rodríguez Guillermo , González-López Borja , Pesce Lourdes 
Published: April 2022

Hombre de 60 años que ingresa en Medicina Interna por dolor abdominal agudo, detectándose en TC abdominal con contraste intravenoso trombosis de la arteria hepática común, por lo que se inicia anticoagulación. En el estudio etiológico se detecta anticoagulante lúpico. Durante la evolución requiere la colocación de una endoprótesis vascular por desarrollo de un aneurisma sacular, sin presentar otras complicaciones.
Shock séptico y tóxico secundario a fascitis necrotizante facial por estreptococo betahemolítico del grupo A en un paciente inmunocompetente
Authors: Pérez-Sanz María Teresa , Parra-Virto Alejandro , Alonso-Muñoz Jaime , Carrascosa-Fernández Paula , Demelo-Rodríguez Pablo 
Published: April 2022

Se expone el caso de un varón de 74 años con historia previa de insuficiencia respiratoria global crónica que acude por episodio de fiebre, dolor e inflamación a nivel periorbitario izquierdo. El cuadro clínico progresó de forma muy llamativa en pocas horas, afectando a la hemicara contralateral y extendiéndose hacia región supraclavicular ipsilateral.
Se confirmó la presencia de Streptococcus pyogenes y el paciente requirió tratamiento quirúrgico urgente, donde presentó inestabilidad hemodinámica en forma de shock séptico.
Tratamiento endovascular del síndrome postrombótico crónico. A propósito de un caso
Authors: Pérez-Catalán Ignacio , Gascón-Ramón Ginés , García-Vila José H. , Roig-Martí Celia , Montañana-Rosell Neus 
Published: April 2022

Paciente de 44 años que en 1994 sufrió un primer episodio de trombosis venosa profunda ilio-femoral izquierda secundaria a un accidente de tráfico. Posteriormente presenta múltiples recidivas trombóticas tratadas con anticoagulación. Tras ser diagnosticado de síndrome postrombótico crónico grave, en 2017 se realiza una recanalización mediante angioplastia y posterior colocación de stent con una mejoría importante tanto morfológica como sintomática. Supone el primer caso de síndrome postrombótico crónico de tan larga evolución tratado mediante abordaje endovascular en la provincia de Castellón.