bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Authors: Dandekar T , Beyer K , Bork P , Kenealy M R , Pantopoulos K , Hentze M , Sonntag-Buck V , Flouriot G , Gannon F , Schreiber S 
Published: July 2002

Abstract
MOTIVATION: The untranslated regions (UTRs) of mRNA upstream (5'UTR) and downstream (3'UTR) of the open reading frame, as well as the mRNA precursor, carry important regulatory sequences. To reveal unidentified regulatory signals, we combine information from experiments with computational approaches. Depending on available knowledge, three different strategies are employed. RESULTS: Searching with a consensus template, new RNAs with regulatory RNA elements can be identified in genomic screens. By this approach, we identify new candidate regulatory motifs resembling iron-responsive elements in the 5'UTRs of HemA, FepB and FrdB mRNA from Escherichia coli. If an RNA element is not yet defined, it may be analyzed by combining results from SELEX (selective enrichment of ligands by exponential amplification) and a search of databases from RNA or genomic sequences. A cleavage stimulating factor (CstF) binding element 3 of the polyadenylation site in the mRNA precursor serves as a test example. Alternatively, the regulatory RNA element may be found by studying different RNA foldings and their correlation with simple experimental tests. We delineate a novel instability element in the 3'UTR of the estrogen receptor mRNA in this way. AVAILABILITY: Strategy, methods and programs are available on request from T.Dandekar. CONTACT: dandekar@embl-heidelberg.de
Oriloc: prediction of replication boundaries in unannotated
bacterial chromosomes
Authors: Frank A. C. , Lobry J. R. 
Published: July 2002

Abstract
Summary: A program called Oriloc has been developed for the prediction of bacterial replication origins. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer 2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio.
Availability: The ANSI C source code is freely available for academic use at ftp://pbil.univ-lyon1.fr/pub/logiciel/oriloc/oriloc.c.
Contact: lobry@biomserv.univ-lyon1.fr
Supplementary information: ftp://pbil.univ-lyon1.fr/pub/logiciel/oriloc/oriloc.ps
* To whom correspondence should be addressed.
Pharmacokinetics and elimination of moxifloxacin after oral and intravenous administration in man
Authors: Stass H. , Kubitza D. 
Published: July 2002

Abstract
The pharmacokinetics of moxifloxacin and its metabolites M1 (sulpho-compound) and M2 (acyl-glucuronide) were characterized in 12 healthy male volunteers in an open, randomized, crossover study. After an overnight fast the volunteers were given a single 400 mg dosage of moxifloxacin either as a tablet or a 1 h infusion with a washout phase of at least 1 week between the two treatments. Multiple plasma, faeces and urine samples were collected for the analysis of moxifloxacin and metabolites using validated HPLC with fluorescence detection. The AUC for both formulations was comparable with bioequivalence criteria fulfilled, with Cmax after oral treatment approximately 31% lower. Following oral administration, absorption was fast with low to medium variability (mean dissolution and absorption time 2.4 h). The absolute bioavailability was 86%. The excretion of moxifloxacin and its metabolites was quantified in a subset of eight subjects. More than 96% of the dose was recovered from urine and faeces after oral dosing, and &gt;98% following iv administration of the drug. M1, which is strongly bound to plasma proteins (90%), was mainly eliminated into faeces (approximately 37–38% of the administered dose) and to a minor extent into urine (2.5% of the administered dose) by active tubular secretion. M2 (only 5% bound to plasma protein) was only found in urine, where it amounted to approximately 14% of the dose. Plasma concentrations of the metabolites were much lower than those of the parent compound. Moxifloxacin was well tolerated with few adverse events and no clinically relevant changes in laboratory values.
Pharmacodynamics of levofloxacin and ofloxacin against Streptococcus pneumoniae
Authors: Bauernfeind A. 
Published: July 2002

Abstract
The aim of this study was to compare the bactericidal efficacy of levofloxacin and ofloxacin against Streptococcus pneumoniae at different dosage regimens for both agents. An in-vitro pharmacodynamic model was used. Levofloxacin kinetics of 500 mg, administered od or bd, were compared with ofloxacin kinetics of 400 mg od or bd. Killing by 3 log 10 (99.9%) was achieved up to an MIC of 0.5 mg/L (500 mg od) or 1 mg/L (500 mg bd). For levofloxacin killing of S. pneumoniae was unimpaired in mixed cultures with Haemophilus influenzae. For ofloxacin, killing by 2 log 10 was achieved up to an MIC of 0.5 mg/L for 400 mg od and up to an MIC of 1 mg/L for 400 mg bd. Killing by 3 log 10 was not achievable by 400 mg od, but was achieved up to an MIC of 0.5 mg/L for 400 mg bd. Killing of S. pneumoniae with identical MICs of levofloxacin was not influenced by their susceptibility to penicillin G. These data, together with the two-fold higher activity of levofloxacin in comparison with ofloxacin, indicate good therapeutic perspectives for levofloxacin over ofloxacin in the treatment of S. pneumoniae infections.
Origins of the
HIVs
and the
AIDS
Outbreaks
Authors: Schneider William H 
Published: April 2022

Abstract

The AIDS pandemic was caused by human immunodeficiency virus (HIV) type 1 group M (HIV‐1M). It is not widely appreciated that there are three other HIV outbreaks that emerged independently in different regions of Africa during the last century. To date, 13 HIV groups have been discovered, but only four of which became major outbreaks to varying degrees. HIV‐1M is responsible for 90% of over 35 million deaths, and the other three epidemic HIVs are estimated to have infected from 25 000 to 750 000 people each. A handful of key determinants explain how and why this happened, including human interaction with the simian sources from which the HIVs emerged, but much more important were new ways that people spread the viruses to one another. The latter included population movement and urbanization, changes in sexual relations, war, and above all new medical procedures (unsterile needles and inadequately tested blood transfusions). The emergence of the viruses and their epidemic spread was not the result of a random mutation but rather depended upon the combination of specific circumstances at different places and times. The AIDS pandemic was not a chance, natural occurrence; it is much more accurately described as a (hu)man‐made disaster.

Key Concepts

The global AIDS pandemic was caused by multiple human immunodeficiency viruses.

The HIVs emerged from different simian immunodeficiency viruses (SIVs) independently in two widely separated regions and at different times, mainly during the early and mid‐twentieth century.

Broader understanding of historical, social, and cultural circumstances is necessary to explain how and why these viruses emerged and became pandemic.

The most important new circumstances causing the emergence of HIV epidemic viruses in the twentieth century were those that facilitated passage of pathogens between humans.

In addition to population movement, urbanization, and changing sexual relations, the most ubiquitous new developments increasing the possibility of adapting viruses to humans were blood transfusions and injections against diseases or for mass vaccination campaigns with insufficiently sterilized needles which were contaminated with as yet undiscovered viruses.
Autosomal Recessive Parkinson' Disease Related to Parkin (
PARK2
) Mutations
Authors: Hatano Taku , Ueno Shin‐Ichi , Okuzumi Ayami , Mori Akio , Oji Yutaka , Hattori Nobutaka 
Published: April 2022

Abstract

Parkinson disease (PD) is a common movement disorder caused by loss of dopaminergic neuronal cells. The molecular mechanisms underlying neuronal degeneration in PD remain unknown; however, it is clear that genetic factors contribute to its pathogenesis. Over 20 genetic loci and causative genes have been identified so far, and many studies have examined their effects on monogenic and sporadic forms of PD. The encoded proteins participate in several cellular functions, including membrane trafficking, and protein and lipid degradation.

Mutations in parkin (
PARK2
) are the most common cause of autosomal recessive early‐onset PD. Parkin functions as an E3 ubiquitin ligase, which monoubiquitinates and polyubiquitinates target proteins. Consequently, parkin participates in multiple cellular processes, such as protein degradation, mitochondrial function, membrane trafficking, lipid metabolism and endoplasmic reticulum stress. Parkin can interact with other familial PD‐associated proteins, possibly within a common pathway that leads to nigral degeneration. There is evidence of a PINK1/parkin pathway involving autophagic mitochondrial degradation. Recent investigations involving imaging and blood biomarkers revealed several alterations associated with parkin dysfunction.

Key Concepts

Parkinson disease
(
PD
) is the second most frequent neurodegenerative disease after Alzheimer disease.

Approximately 5% of PD patients have a clear familial aetiology, exhibiting a classical recessive or dominant Mendelian mode of inheritance.

Parkin (
PARK2
) is the most prevalent gene associated with early‐onset Parkinsonism and is associated with approximately 50% of recessive familial patients with an onset under 45 years of age.

Abnormal imaging and blood biomarkers are associated with parkin dysfunction.

Parkin functions as an E3 ubiquitin ligase, which participates in the
ubiquitin–proteasome
(
Ub‐Pr
) system.

Collaboration between parkin and PINK1 promotes the autophagic degradation of damaged mitochondria.

Parkin can participate in several pathways that lead to dopaminergic neuronal degeneration, such as the Ub‐Pr system, autophagic protein degradation, the mitochondrial quality control system, the membrane trafficking system and lipid metabolism.
Exceptional Preservation of Fossil Soft Tissues
Authors: Clements Thomas , Gabbott Sarah 
Published: April 2022

Abstract

Exceptionally preserved soft tissues yield much more information about ancient organisms than skeletal remains alone. These fossils are rare, because, generally, the postmortem processes of decay rapidly strip away information from a carcass before preservation can occur. However, if certain environmental conditions are present that slow the normal recycling of organic material, there is a possibility that soft tissues can become geologically stabilised by the processes of mineralisation or maturation. In order to understand the biological, environmental, and geological factors that control soft tissue preservation, palaeobiologists combine the study of fossil material with laboratory experiments that decay organisms in strictly controlled environmental conditions. These experimental investigations have enhanced our understanding of the inherent biases of the fossil record, and allow more accurate reconstructions of ancient organisms and a better understanding of evolution and ecology. New techniques and cutting‐edge analytical equipment are revolutionising the field, opening up exciting new avenues of palaeontological research such as the identification of fossilised pigments and palaeoproteins.

Key Concepts

Fossils that have soft tissues generally provide more information about ancient organisms than skeletal remains alone.

Organisms undergo varying amounts of decay prior to preservation.

Conservation‐Lagerstätten are sites where depositional environmental conditions disrupted the normal rapid recycling of organic material (e.g. decay) allowing soft tissues to preserve.

Conservation‐Lagerstätten are important not only because they preserve soft‐bodied organisms that are extremely rare in the fossil record but also because they tend to preserve a great diversity of organisms, making them vital windows into the ancient past.

Many sedimentary Conservation‐Lagerstätten share characteristics of rapid burial, low oxygen, and the early onset of diagenetic processes such as mineralisation and/or maturation.

Another type of Conservation‐Lagerstätten are natural traps, such as amber or permafrost, but comparatively, these are geologically young.

The study of burial and preservation is termed taphonomy.

Since the 1980s, laboratory experiments have been undertaken to understand the drivers of soft‐tissue preservation.

Rather than recreating fossils or ancient environments in the lab, robust taphonomic experiments investigate the effect of discrete variables on taphonomic processes.

New avenues in taphonomic investigation are opening up with the advent of new technology and laboratory equipment.
High‐Performance Freshwater Harvesting System by Coupling Solar Desalination and Fog Collection with Hierarchical Porous Microneedle Arrays
Authors: Zhou Wei , Zhou Cailong , Deng Chengfei , Chen Li , Zeng Xinjuan , Zhang Yaoxin , Tan Luxi , Hu Baoshan , Guo Shuai , Dong Lichun , Tan Swee Ching 
Published: April 2022

AbstractThe maximizing daily freshwater yield on the ocean surface necessitates all‐day water harvesting technologies and materials. This is realizable by taking advantage of the natural sunlight and humid air, which can drive daytime solar desalination and nighttime fog collection, respectively. To this end, two types of hierarchically porous microneedle array structures, which demonstrate superior capabilities for efficient fog capturing and photothermal evaporation, respectively, are prepared. The gel‐forged microneedle arrays with Janus wettability are fabricated via a simple and controllable top‐down micro‐molding process on a porous platform, and porosity within microneedles is further achieved readily by additional freeze‐drying treatment. The developed microneedle structure shows an ultrahigh fog harvesting rate up to 30.5 kg m−2 h−1, enabling high flux water droplet harvesting from moisture during nighttime. In the daytime, a solar evaporation rate of 2.46 kg m−2 h−1 is realized due to the increased evaporative area of the porous microneedle arrays and enhanced photothermal conversion. By uniting these two water‐harvesting routes, a daily cycle can ideally deliver an overall water yield close to 200 kg m−2, which will offer a promising solution for sustaining future low‐cost and decentralized clean water production.
A Real‐Time Self‐Adaptive Thermal Metasurface
Authors: Guo Jun , Xu Guoqiang , Tian Di , Qu Zhiguo , Qiu Cheng‐Wei 
Published: April 2022

AbstractEmerging metamaterials have served as an efficient strategy for the realization of unconventional heat control and management using structural thermal properties, and many functional thermal metadevices have been investigated. However, thermal functions are usually fixed or limited in the switching range. Thus far, real‐time thermal regulation is elusive for thermal metamaterials because of deterministic artificial metastructures and uncontrollable phase transitions, coupled with the absence of dynamic adaptability. Here, a self‐adaptive metasurface platform to implement programmable thermal functions via the automatic evolution of thermoelectric heat sources and real‐time control of the driven voltage is reported. The proof‐of‐concept smart platform experimentally demonstrates arbitrary switching between elaborate thermal patterns consolidated into an active thermoelectric element matrix. Further, thermal pixels and feedback control systems are integrated into printed circuit boards, resulting in self‐adaptability to any thermal requirements. This study sets up a new paradigm for arbitrary transitions between exquisite thermal patterns and is expected to pave the way for real‐time thermal management in a programming formation.
MOF–COF “Alloy” Membranes for Efficient Propylene/Propane Separation
Authors: Liu Yutao , Wu Hong , Li Runlai , Wang Jianyu , Kong Yan , Guo Zheyuan , Jiang Haifei , Ren Yanxiong , Pu Yunchuan , Liang Xu , Pan Fusheng , Cao Yu , Song Shuqing , He Guangwei , Jiang Zhongyi 
Published: April 2022

AbstractMolecular‐sieving membranes from metal–organic frameworks (MOFs) are promising candidates for separating olefin/paraffin mixtures, a critical demand in sustainable chemical processes and a grand challenge in molecular separation. Currently, the inherent lattice flexibility of MOFs severely compromises their precise sieving ability. Here, a proof‐of‐concept of “alloy” membranes (AMs), which are fabricated by incorporating quaternary ammonium (QA)‐functionalized covalent organic frameworks (COFs) into a zeolitic imidazolate framework‐8 (ZIF‐8) matrix is demonstrated. The Coulomb force between the COFs and the ZIF‐8 restricts the linker rotation of the ZIF‐8, generating a distinct alloying effect, by which the lattice rigidity of ZIF‐8 can be conveniently tuned through varying the content of the COFs, similar to the flexible‐to‐rigid transition in aluminum alloy manufacturing. Such an alloying effect confers the AM's superior propylene/propane separation performance, with a propylene/propane separation factor surpassing 200 and a propylene permeance of 168 GPU. Hopefully, the AMs concept and the concomitant alloying effect can update the connotation of mixed matrix membranes and stimulate the re‐envisioning about the design paradigm and development of advanced membranes for energy‐efficient separations.
2D SnSe Cathode Catalyst Featuring an Efficient Facet‐Dependent Selective Li2O2 Growth/Decomposition for Li–Oxygen Batteries
Authors: Zhang Guoliang , Li Gaoyang , Wang Jun , Tong Hui , Wang Jianchuan , Du Yong , Sun Shuhui , Dang Feng 
Published: April 2022

Abstract2D materials are attracting much attention in the field of cathode catalysts for lithium–oxygen batteries (LOBs) due to their layered structure, unique electronic properties, and high stability. However, different stacking layer structures trigger different catalytic capabilities in LOBs. In this work, tin selenide nanosheets with a black phosphorus‐like 2D structure are synthesized and used as the cathode catalyst for LOBs. SnSe nanosheets with exposed stack (200) facets and stack edge facets exhibit superior specific capacity over 20 783 mAh g−1 and ultralong cycle stability over 380 cycles at 500 mA g−1 in LOBs. This demonstrates that the growth of discharge products is mainly concentrated on the 2D surface (200) facets, rather than the stack edge facets. Experimental and theoretical studies reveal that the confined adsorption of Li2O2 on the stack edge facets of SnSe, due to the 2D layer structure and the unique electron distribution, restricts the growth of discharge products. The 2D surface facets of SnSe benefit for the formation and stabilization of LiO2 intermediates, leading to the efficient formation/decomposition of discharge products. The findings provide in‐depth insight into the elusive electrocatalytic mechanism for 2D layer‐structures materials in LOBs.
Manipulative repertoire of bonobos (Pan paniscus) in spontaneous feeding situation
Authors: Gérard Caroline , Bardo Ameline , Guéry Jean P. , Pouydebat Emmanuelle , Simmen Bruno , Narat Victor 
Published: April 2022

AbstractComparative behavioral studies of hand use amongst primate species, including humans, have been central in research on evolutionary mechanisms. In particular, the manipulative abilities of our closest relatives, the chimpanzee (Pan troglodytes), have been widely described in various contexts, showing a high level of dexterity both in zoo and in natural conditions. In contrast, the study of bonobos' manipulative abilities has almost exclusively been carried out in experimental contexts related to tool use. The objective of the present study is to describe the richness of the manipulative repertoire of zoo‐housed bonobos, in a spontaneous feeding context including various physical substrates to gain a larger insight into our evolutionary past. Our study describes a great variety of grasping postures and grip associations in bonobos, close to the range of manipulative repertoire in chimpanzees, confirming that the two species are not markedly different in terms of cognitive and morphological constraints associated with food manipulation. We also observed differences in manipulative behaviors between juveniles and adults, indicating a greater diversity in grip associations and grasping postures used in isolation with age, and a sex‐biased use of tools with females using tools more often than males. These results are consistent with the previous results in the Pan genus and reinforce the hypothesis that the evolutionary mechanisms underlying the flexibility of manipulative behaviors are shared by both species and that these ecological strategies would have already evolved in their common ancestor.
Tau‐induced deficits in nonsense‐mediated mRNA decay contribute to neurodegeneration
Authors: Zuniga Gabrielle , Levy Simon , Ramirez Paulino , De Mange Jasmine , Gonzalez Elias , Gamez Maria , Frost Bess 
Published: April 2022

AbstractIntroductionWhile brains of patients with Alzheimer's disease and related tauopathies have evidence of altered RNA processing, we lack a mechanistic understanding of how altered RNA processing arises in these disorders and if such changes are causally linked to neurodegeneration.MethodsUsing Drosophila melanogaster models of tauopathy, we find that overall activity of nonsense‐mediated mRNA decay (NMD), a key RNA quality‐control mechanism, is reduced. Genetic manipulation of NMD machinery significantly modifies tau‐induced neurotoxicity, suggesting that deficits in NMD are causally linked to neurodegeneration. Mechanistically, we find that deficits in NMD are a consequence of aberrant RNA export and RNA accumulation within nuclear envelope invaginations in tauopathy. We identify a pharmacological activator of NMD that suppresses neurodegeneration in tau transgenic Drosophila, indicating that tau‐induced deficits in RNA quality control are druggable.DiscussionOur studies suggest that NMD activators should be explored for their potential therapeutic value to patients with tauopathies.
A 3D‐printable device allowing fast and reproducible longitudinal preparation of mouse intestines
Authors: DeLucia Beckey , Samorezov Sergey , Zangara Megan T. , Markley Rachel L. , Osborn Lucas J. , Schultz Karlee B. , McDonald Christine , Claesen Jan 
Published: April 2022

AbstractAccurate and reproducible analysis of murine small and large intestinal tissue is key for preclinical models involving intestinal pathology. Currently, there is no easily accessible, standardized method that allows researchers of different skill levels to consistently dissect intestines in a time‐efficient manner. Here, we describe the design and use of the 3D‐printed “Mouse Intestinal Slicing Tool” (MIST), which can be used to longitudinally dissect murine intestines for further analysis. We benchmarked the MIST against a commonly used procedure involving scissors to make a longitudinal cut along the intestines. Use of the MIST halved the time per mouse to prepare the intestines and outperformed alternative methods in smoothness of the cutting edge and overall reproducibility. By sharing the plans for printing the MIST, we hope to contribute a uniformly applicable method for saving time and increasing consistency in studies of the mouse gastrointestinal tract.