bluuebunny/crossref_metadata_2025_split huggingface dataset:
PESTICIDES AND THE FOOD SUPPLY
Authors: Richardson L. A. , Foter Milton J. 
Published: November 2018

Summary
The use of chemical pest control agents undoubtedly constitutes a calculated risk; nonetheless, the proper use of these agents results in benefits which, at the present time, far outweigh the known potential hazards. Considerable care must be exercised in the selection, storage, and use of pesticide chemicals and in the disposition of the empty containers. Since virtually all pesticides are more or less toxic to man and cumulative and potentiation characteristics are not well defined, regulation through registration and the establishment of residue tolerances is essential. Scientists recognize that the adequate production and preservation of food and fiber and the protection of human health require the use of chemical pesticides. Federal, state, and local health agencies and the food and chemical industries are striving through research and residue surveillance to show the effect of pesticides on human beings and to provide alternative means of pest control. Until these chemical agents are replaced by less toxic means of control, the use of pesticides will continue. As in any scientific venture, the benefit-hazard ratio in the use of pesticides may never be completely established, but we must act on the best available evidence.
A STATEWIDE_SURVEY OF FREEZING POINTS OF AUTHENTIC MILK SAMPLES1,2
Authors: Bradshaw P. L. , Marshall R. T. , Edmondson J. E. 
Published: November 2018

Summary
Eigty-three authentic samples were taken from the mixed herd milk of dairies located in eight areas of the State of Mississippi during an eight-month period. The range of freezing points observed was wider than expected based on the recognized upper limit of −0.530 C. Eleven percent of the samples would have been termed adulterated based on this accepted standard. The mean freezing point was −0.536 C and the standard deviation −0.006 C. The data showed a moderately acceptable normal curve fit. But the true distribution appeared somewhat skewed, indicating that factors other than normal differences between animals tend to force the freezing point up. Variation between laboratories was small. The mean test deviation was slightly more than 0.001 C.
SOME FACTORS AFFECTING THE CORRELATION OF METHYLENE BLUE REDUCTION TIMES AND STANDARD PLATE COUNTS OF RAW MILK
Authors: Brazis A. Richard , Black L. A. 
Published: November 2018

Summary
Standard plate and psychrophilic bacterial counts, on 312 samples of milk collected from farm bulk tanks and milk cans, were compared with methylene blue reduction times using the standard procedure or preliminary incubation of samples at 55 F for 18 hr prior to testing. When psychrophilic bacterial counts were less than 100,000/ml, according to standard plate counts a high proportion of methylene blue reduction times were properly classified. However, psychrophilic bacterial counts greater than 100,000/ml did not significantly decrease reduction times, thus a high proportion of such milks was not properly classified by methylene blue reduction times. The proportion of misclassification of samples having standard plate counts in excess of 200,000/ml and methylene blue reduction times of 5 and 6 hr was determined.
Dynamically coupling full Stokes and shallow shelf approximation for marine ice sheet flow using Elmer/Ice (v8.3)
Authors: van Dongen Eef C. H. , Kirchner Nina , van Gijzen Martin B. , van de Wal Roderik S. W. , Zwinger Thomas , Cheng Gong , Lötstedt Per , von Sydow Lina 
Published: November 2018

Abstract. Ice flow forced by gravity is governed by the full Stokes (FS) equations, which are computationally expensive to solve due to the nonlinearity introduced by the rheology. Therefore, approximations to the FS equations are commonly used, especially when modeling a marine ice sheet (ice sheet, ice shelf, and/or ice stream) for 103 years or longer. The shallow ice approximation (SIA) and shallow shelf approximation (SSA) are commonly used but are accurate only for certain parts of an ice sheet. Here, we report a novel way of iteratively coupling FS and SSA that has been implemented in Elmer/Ice and applied to conceptual marine ice sheets. The FS–SSA coupling appears to be very accurate; the relative error in velocity compared to FS is below 0.5 % for diagnostic runs and below 5 % for prognostic runs. Results for grounding line dynamics obtained with the FS–SSA coupling are similar to those obtained from an FS model in an experiment with a periodical temperature forcing over 3000 years that induces grounding line advance and retreat. The rapid convergence of the FS–SSA coupling shows a large potential for reducing computation time, such that modeling a marine ice sheet for thousands of years should become feasible in the near future. Despite inefficient matrix assembly in the current implementation, computation time is reduced by 32 %, when the coupling is applied to a 3-D ice shelf.
Biological soil crusts inhibit seed germination in a mesic pine barren ecosystem
Authors: Gilbert Jessica A. , Corbin Jeffrey D. 
Published: November 2018

Aims - Biological soil crusts (BSCs) are known to affect plants’ germination and seedling establishment, but the ecological role of BSCs in more mesic climates are not so well-known. We tested the effects of moss-crusted versus uncrusted soils on seed germination dynamics in a temperate pine barren ecosystem.
Methods - We conducted a 35-day laboratory assay of seed germination on moss-crusted soils versus uncrusted soils from the Albany (NY) Pine Bush Preserve. We tested total seed germination and the number of days to 50% of total germination (T50) of two herbaceous perennial forb species in each soil type.
Results - Three and five times more seeds germinated on uncrusted soil than on crusted soil for bush clover (Lespedeza capitata) and wild lupine (Lupinus perennis), respectively. Seeds of both species also germinated approximately 10 days earlier on uncrusted soil than on crusted soil.
Conclusions - This study, and others in similar habitats, show that BSCs in mesic ecosystems can influence germination and other early life-history stages of plants. We hope that further study of the interactions between BSCs and vascular plants in mesic climates will contribute to our understanding of the ecology of BSCs outside the arid and semiarid climates where they are more extensively studied.
A comparison of student performance and satisfaction between a traditional and integrative approach to teaching an introductory radiology course on the extremities
Authors: Jarrett-Thelwell Fiona D. , Burke Jeanmarie R. , Poirier Jean-Nicolas , Petrocco-Napuli Kristina 
Published: November 2018

Objective:
The purpose of the study was to compare student performance and student satisfaction ratings for an introductory extremities radiology course taught using 2 different educational methods.

Methods:
One group of students was taught using a traditional face-to-face instruction method, and the other group received an integrative blended-learning approach. A multivariate analysis of scores on lecture and laboratory examinations was performed to detect differences in student performance between the 2 methods. An independent t test was performed to compare the final course averages between the 2 methods. χ2 Analysis was used to compare the distribution of letter grades and levels of satisfaction between the 2 groups.

Results:
Test scores were higher for the integrative approach than for the traditional face-to-face method (p &lt; .05). However, the differences were not meaningful, as the greatest improvement in correct responses was only for 2 questions. Students appeared to be more satisfied with the integrative approach when compared to the traditional method (p &lt; .05).

Conclusion:
Student satisfaction with the educational delivery methods in an introductory extremities radiology course using an integrative approach was greater than for the traditional face-to-face instruction method. Student performance was similar between the 2 cohorts.
Quantifying Colocalisation in Biological Fluorescence Microscopy
Authors: Oheim Martin , Brunstein Maia 
Published: November 2018

Abstract

One of the basic concepts in biological fluorescence microscopy is the separation of photons from spectrally distinct fluorophores into different colour channels for studying questions concerning the colocalisation, coclustering or interaction of fluorescently labelled proteins, organelles or membranes on fluorescence images. The quantitative use of colocalisation information, however, is not without pitfalls, and the validity of arguments based on the comparison of dual‐colour fluorescence images depends on which molecular targets are labelled and how; which combinations of fluorophores, excitation wavelengths and filters are chosen; how images are acquired and at which spatiotemporal resolution and by which means they are analysed. Unfortunately, no consensual metrics for quantifying colocalisation has emerged. Interrogations as to how colocalisation is best quantified currently make surface again in the context of superresolution microscopies that are increasingly being used in the life sciences. We focus on the practice of the colocalisation imaging workflow and point out problematic steps, guiding the reader to make more informed statements beyond the common ‘red‐plus‐green‐equals‐yellow’ approach.

Key Concepts

Colocalisation measurements are only as good as the raw images they are calculated from – hence, the entire imaging workflow must be understood and quality controlled.

Molecules do not occupy the same place. They are, by definition, not ‘colocalised’. Their imperfect images overlap, and both their proximity and the available spatial resolution determine the amount of colocalisation.

More often than not, colocalisation will be partial, and therefore only interpretable with some reference or when compared among conditions.

Measures of colocalisation need to be held against the random colocalisation arising when structures are placed independently at the same density on an equivalent area.

Colocalisation measurements are more meaningful when presented along with positive and negative controls and when the fluctuation of colocalisation within subfields of view, or – for live cells – over time, is reported.

Fluorophore concentrations, acquisition parameters, intensity ranges and image processing and segmentation rules should be made explicit to allow comparison of data across experiments and laboratories.

Colocalisation studies must always be considered relative to the available spectral, spatial (and for live cells also temporal) resolution, which needs to be explicitly stated.
Can There Be a ‘Liberal Eugenics’?
Authors: Davis Dena S 
Published: November 2018

AbstractIt is possible to have a liberal eugenics, in which certain population outcomes are neither coerced nor predetermined, but driven by individual parental choice. There is, however, a paradox. There will always be disabled people among us, if not as a result of genetic disease, then from trauma, disease and old age. How do we create a society where parents are free to choose not to give birth to disabled children, but where we still value and support the disabled members of our community?Key ConceptsThe debate over ‘liberal eugenics’ is actually a number of debates, made murkier by semantic confusion.It is possible to have a liberal eugenics, in which certain population outcomes are neither coerced nor predetermined, but driven by individual parental choice.Authoritarian eugenics was scientifically ignorant, used coercive means and treated people as means to eugenic ends.Liberal genetics is propelled primarily by individual prospective parents making free choices.‘Eugenic’ efforts have shifted from a focus on those who should not reproduce to those who should not be produced.While early eugenics focused on poor and marginalised people, it is now wealthier people who have better access to scientific means of preventing the birth of disabled children.
Interleukin‐1
Authors: Etti Azulay E , Assy Nimer , Idan Cohen 
Published: November 2018

Abstract

The interleukin‐1 (IL‐1) family of ligands and receptors plays a central role in the generation and regulation of inflammation as a part of the immune response. IL‐1 molecules are best known as members of the pro‐inflammatory protein family called cytokines. They have been shown to play a role, not only during inflammation, but also in influencing additional physiological and pathological functions such as auto‐immune diseases, malignancies and many others. Moreover, the biological balance between pro‐inflammatory and inhibitory activities is crucial, since any shift in IL‐1 family expression has the potential to cause disease.

Key Concepts

Interleukin‐1 proteins play a central role in the generation and regulation of inflammatory processes.

The IL‐1α and IL1‐β ligands are pro‐inflammatory cytokines. IL‐1Ra and IL‐1RII are natural inhibitors of IL‐1 signalling.

Shifts in the balance between agonistic and antagonistic signals of IL‐1 family members are crucial for a proper immune response.

Changes in production and secretion of IL‐1 proteins, which determine the balance between activating and neutralising IL‐1R signalling, are widely associated with many human diseases.

IL‐1 neutralisation is now considered as an attractive therapeutic strategy for many diseases, including cancer.
Molecular Genetics of
B
irt–
H
ogg–
D
ubé Syndrome
Authors: Schmidt Laura S 
Published: November 2018

Abstract

Birt–Hogg–Dubé (BHD) syndrome is an autosomal dominant hereditary cancer disorder that predisposes at‐risk individuals to develop cutaneous fibrofolliculomas, pulmonary cysts, spontaneous pneumothoraces and kidney tumours. Germline mutations in the
FLCN
gene on chromosome 17 are responsible for BHD. BHD‐associated kidney tumours are most frequently hybrid oncocytic tumours or chromophobe renal carcinoma and show inactivation of the wild‐type
FLCN
allele either by somatic mutation or chromosomal loss, confirming that
FLCN
is a classic tumour suppressor. The FLCN protein interacts with two binding partners, FNIP1 and FNIP2, and with AMPK – an important negative regulator of mTOR. Studies in
Flcn
‐deficient animal models support a role for FLCN in modulating mTOR activity. Emerging evidence suggests that FLCN interacts in a number of molecular pathways important for cell homeostasis that are often dysregulated in cancer including regulation of TFE3/TFEB transcriptional activity, amino acid‐dependent mTOR activation through Rag GTPases, TGF‐β signalling, PGC1‐α‐driven mitochondrial biogenesis and autophagy.

Key Concepts

Birt–Hogg–Dubé (BHD) syndrome is an autosomal dominant hereditary syndrome that predisposes at‐risk individuals to develop cutaneous fibrofolliculomas, pulmonary cysts, spontaneous pneumothorax and increased risk for kidney tumours.

Germline mutations in the
FLCN
gene on chromosome 17 are responsible for Birt–Hogg–Dubé syndrome.

BHD‐associated kidney tumours are characterised by inactivation of the wild‐type copy of
FLCN
by somatic mutation or loss of chromosome 17p sequences confirming that
FLCN
is a classic tumour suppressor gene that follows the two‐hit model of tumourigenesis.

Kidney tumours that develop in BHD‐affected individuals are most frequently hybrid oncocytic tumours or chromophobe renal carcinoma.

The FLCN protein interacts with two novel binding partners, FNIP1 and FNIP2, and also with AMPK, an important negative regulator of mTOR.

Studies in
Flcn
‐deficient animal models support a role for FLCN in modulating mTOR activity.

Emerging evidence suggests that FLCN may interact in a number of molecular pathways important for cellular homeostasis that are often dysregulated in cancer.
G
‐Quadruplexes (
G4s
)
Authors: Richter Sara N 
Published: November 2018

Abstract

Guanine‐rich regions of nucleic acids can fold into G‐quadruplex, a secondary structure formed by four strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). In the G‐quadruplex, guanines bind via Hoogsteen hydrogen bonds to yield the G‐quartet. Two or more G‐quartets stack on top of each other to form the G‐quadruplex, which can adopt different conformations, based both on the nature and orientation of the strands and on environmental factors such as cations. Both DNA and RNA G‐quadruplexes are found in biological systems: They have been computationally predicted and experimentally demonstrated by several methods in the genomes of several organisms, including humans, other eukaryotes, bacteria and viruses. G‐quadruplexes in the human cell genome are found in pivotal genomic regions, where they mainly act as regulatory elements. Several proteins process the G‐quadruplex. G‐quadruplex ligands that stabilise these structures are investigated against several diseases, as cancer and viral infections. In turn, G‐quadruplexes can themselves act as therapeutics.

Key Concepts

G‐quadruplexes are noncanonical nucleic acid structures that form in guanine‐rich sequences.

G‐quadruplexes can form both in the DNA and RNA and are structurally extremely heterogeneous.

Both computational and experimental methods have shown the presence of G‐quadruplexes in the genome of humans and other organisms, such as bacteria and viruses.

G‐quadruplexes mainly function as epigenetic regulatory elements.

G‐quadruplexes interact with a diverse array of cellular proteins, which induce, stabilise or destabilise them.

Several methods have been developed to study the G‐quadruplex conformation in short oligonucleotides, longer sequences and whole genomes.

Compounds that bind the G‐quadruplex are being studied as inhibitors of important human diseases such as cancer and infective diseases.

G‐quadruplex‐folded aptamers have therapeutic potential.
Novel Strategies Targeting
G
‐Protein‐Coupled Receptors: An Overview
Authors: García‐Cárceles Javier 
Published: November 2018

Abstract

G‐protein‐coupled receptors (GPCRs) represent the largest group of cell surface receptors encoded by the human genome (∼2%) and have been associated to a multitude of human disorders, which makes them the focus of attention of many drug discovery programs. Traditionally, the development of drugs that target GPCRs has been focused on finding agonists or antagonists that displace the natural or endogenous ligand to activate or inhibit the receptor. Emerging knowledge of structure and physiological functions of GPCRs has begun to alter the approaches to drug discovery. Thus, over the past two decades, novel strategies such as the development of biased and bitopic ligands, allosteric modulators, pepducins or ligands targeting GPCR heteromers have appeared. Some of these new approaches have proved to be productive, yielding molecules currently in clinical trials or even marketed.

Key Concepts

GPCRs are cell membrane proteins essential for the survival of eukaryotic cells and they can be classified in four different classes based on their amino acid sequence.

GPCRs are responsible for the realisation of cell functions through the transduction of a wide range of extracellular stimuli such as light, hormones, odours, peptides and neurotransmitters among others.

GPCRs are associated with a multitude of human disorders, in fact, medicines targeting these receptors comprise 35% of the drugs on the market.

Traditional approaches targeting GPCRs, that is development of agonists or antagonists that compete with the orthosteric or endogenous ligand, have become ineffective developing new drugs.

Selectivity across subtypes in a certain receptor family has been the major issue in order to obtain safer drugs.

The emergence of new and more sensitive pharmacological, biochemical and biophysical techniques have helped in designing novel strategies targeting GPCRs. The publication of crystal structures of GPCRs bound to various kind of ligands have been particularly helpful in determining the molecular basis of ligand binding.
Lateral Root Formation: Building a Meristemde novo
Authors: Trinh Chi D , Laplaze Laurent , Guyomarc'h Soazig 
Published: November 2018

AbstractThe complex and adaptable architecture of the plant root system in soil is of paramount importance for crop growth and performance. Root growth depends on the activity of the root apical meristem, an organised population of proliferating progenitor cells continuously replenished from a stem cell niche. Root branching, which greatly contributes to root system architecture in most dicot species, consists ofde novoformation of new root meristems in existing root tissues. This phenomenon illustrates the ability of plants to repeatedly generate new tissues specialised in post‐embryonic continuous growth and greatly impacts the elaboration of the root system architecture and its adaptation to environmental constraints. Here, we review the recent findings and models related to lateral root organogenesis in the dicot speciesArabidopsis thaliana, with emphasis on the mechanisms controllingde novoroot meristem formation. Experimental evidence suggests that critical regulatory modules are common between embryonic and post‐embryonic root meristem organogenesis and that the lateral root formation molecular pathway is in part common with organ regeneration from callus.
MYORG is associated with recessive primary familial brain calcification
Authors: Arkadir David , Lossos Alexander , Rahat Dolev , Abu Snineh Muneer , Schueler‐Furman Ora , Nitschke Silvia , Minassian Berge A. , Sadaka Yair , Lerer Israela , Tabach Yuval , Meiner Vardiella 
Published: November 2018

AbstractObjectiveTo investigate the genetic basis of the recessive form of primary familial brain calcification and study pathways linking a novel gene with known dominant genes that cause the disease.MethodsWhole exome sequencing and Sanger‐based segregation analysis were used to identify possible disease causing mutations. Mutation pathogenicity was validated by structural protein modeling. Functional associations between the candidate gene, MYORG, and genes previously implicated in the disease were examined through phylogenetic profiling.ResultsWe studied nine affected individuals from two unrelated families of Middle Eastern origin. The median age of symptom onset was 29.5 years (range 21–57 years) and dysarthria was the most common presenting symptom. We identified in the MYORG gene, a homozygous c.1233delC mutation in one family and c.1060_1062delGAC mutation in another. The first mutation results in protein truncation and the second in deletion of a highly conserved aspartic acid that is likely to disrupt binding of the protein with its substrate. Phylogenetic profiling analysis of the MYORG protein sequence suggests co‐evolution with a number of calcium channels as well as other proteins related to regulation of anion transmembrane transport (False Discovery Rate, FDR < 10−8) and with PDCD6IP, a protein interacting with PDGFRβ which is known to be involved in the disease.InterpretationMYORG mutations are linked to a recessive form of primary familial brain calcification. This association was recently described in patients of Chinese ancestry. We suggest the possibility that MYORG mutations lead to calcification in a PDGFRβ‐related pathway.