SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Fragment

17

Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, ~15 and ~30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes.

Concepts: Biodiversity, Fragment, Fragmentation, Evolution, Ecology, Forest, Tropical rainforest, Secondary forest

16

This paper examines research on peer review between 1969 and 2015 by looking at records indexed from the Scopus database. Although it is often argued that peer review has been poorly investigated, we found that the number of publications in this field doubled from 2005. A half of this work was indexed as research articles, a third as editorial notes and literature reviews and the rest were book chapters or letters. We identified the most prolific and influential scholars, the most cited publications and the most important journals in the field. Co-authorship network analysis showed that research on peer review is fragmented, with the largest group of co-authors including only 2.1% of the whole community. Co-citation network analysis indicated a fragmented structure also in terms of knowledge. This shows that despite its central role in research, peer review has been examined only through small-scale research projects. Our findings would suggest that there is need to encourage collaboration and knowledge sharing across different research communities.

Concepts: Scientific method, Fragment, Academic publishing, Research, Peer review, Review, Book, Scopus

13

As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known about the status of chimpanzee populations in these fragments.

Concepts: Human, Fragment, Fragmentation, Biology, Sociology, Habitats, Chimpanzee, Orangutan

11

Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called “schools of thought”. We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model’s implications for the design of social institutions fostering interdisciplinarity and participation in science.

Concepts: Scientific method, Fragment, Causality, Sociology, Affect, Science, Philosophy of science, Scientist

11

Glioblastoma (GB) is the most common and aggressive primary brain malignancy, with poor prognosis and a lack of effective therapeutic options. Accumulating evidence suggests that intratumor heterogeneity likely is the key to understanding treatment failure. However, the extent of intratumor heterogeneity as a result of tumor evolution is still poorly understood. To address this, we developed a unique surgical multisampling scheme to collect spatially distinct tumor fragments from 11 GB patients. We present an integrated genomic analysis that uncovers extensive intratumor heterogeneity, with most patients displaying different GB subtypes within the same tumor. Moreover, we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression. We also characterized the clonal organization of each tumor fragment at the single-molecule level, detecting multiple coexisting cell lineages. Our results reveal the genome-wide architecture of intratumor variability in GB across multiple spatial scales and patient-specific patterns of cancer evolution, with consequences for treatment design.

Concepts: Medicine, Gene, Genetics, Cancer, Fragment, Oncology, Evolution, Brain tumor

8

The benthic biota of the Clarion-Clipperton Zone (CCZ, abyssal eastern equatorial Pacific) is the focus of a major research effort linked to possible future mining of polymetallic nodules. Within the framework of ABYSSLINE, a biological baseline study conducted on behalf of Seabed Resources Development Ltd. in the UK-1 exploration contract area (eastern CCZ, ~4,080 m water depth), we analysed foraminifera (testate protists), including ‘live’ (Rose Bengal stained) and dead tests, in 5 cores (0-1 cm layer, >150-μm fraction) recovered during separate megacorer deployments inside a 30 by 30 km seafloor area. In both categories (live and dead) we distinguished between complete and fragmented specimens. The outstanding feature of these assemblages is the overwhelming predominance of monothalamids, a group often ignored in foraminiferal studies. These single-chambered foraminifera, which include agglutinated tubes, spheres and komokiaceans, represented 79% of 3,607 complete tests, 98% of 1,798 fragments and 76% of the 416 morphospecies (live and dead combined) in our samples. Only 3.1% of monothalamid species and 9.8% of all species in the UK-1 assemblages are scientifically described and many are rare (29% singletons). Our results emphasise how little is known about foraminifera in abyssal areas that may experience major impacts from future mining activities.

Concepts: Fragment, Life, Oceanography, Pacific Ocean, Arctic Ocean, Foraminifera, Seabed, Manganese nodule

5

Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfy design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards, and provides a fabrication plan for each fragment.

Concepts: DNA, Gene, Fragment, Molecular biology, Biology, Organism, Species, Part

5

At the site of Marillac, near the Ligonne River in Marillac-le-Franc (Charente, France), a remarkable stratigraphic sequence has yielded a wealth of archaeological information, palaeoenvironmental data, as well as faunal and human remains. Marillac must have been a sinkhole used by Neanderthal groups as a hunting camp during MIS 4 (TL date 57,600 ± 4,600BP), where Quina Mousterian lithics and fragmented bones of reindeer predominate. This article describes three infracranial skeleton fragments. Two of them are from adults and consist of the incomplete shafts of a right radius (Marillac 24) and a left fibula (Marillac 26). The third fragment is the diaphysis of the right femur of an immature individual (Marillac 25), the size and shape of which resembles those from Teshik-Tash and could be assigned to a child of a similar age. The three fossils have been compared with the remains of other Neanderthals or anatomically Modern Humans (AMH). Furthermore, the comparison of the infantile femora, Marillac 25 and Teshik-Tash, with the remains of several European children from the early Middle Ages clearly demonstrates the robustness and rounded shape of both Neanderthal diaphyses. Evidence of peri-mortem manipulations have been identified on all three bones, with spiral fractures, percussion pits and, in the case of the radius and femur, unquestionable cutmarks made with flint implements, probably during defleshing. Traces of periostosis appear on the fibula fragment and on the immature femoral diaphysis, although their aetiology remains unknown. Am J Phys Anthropol, 2014. © 2014 Wiley Periodicals, Inc.

Concepts: Bone, Human, Fragment, Middle Ages, Left-wing politics, Neanderthal, Human evolution, Mousterian

4

Throughout the course of a forensic investigation following an explosive attack, the identification and recovery of tissue fragments is of extreme importance. There are few universally accepted methods to achieve this end. This project aims to explore this issue through the examination of the spatial distribution of the tissue fragments resulting from an explosive event. To address this, a two stage pilot study was conducted: first, a series of controlled explosions on porcine carcases was undertaken. Second, the data produced from these explosions were used to chart the spatial distribution of the tissue debris. In the controlled explosions, 3kg military grade explosive was chosen to create the maximum amount of fragmentation; this level of explosive also prevented the complete disappearance of forensic evidence through evaporation. Additionally, the blast created by military grade explosive is highly powerful and would mean that the maximum possible distance was achieved and would therefore allow the recorded distances and pattern spread to be a guideline for forensic recovery of associated with an explosive amount of an unknown size and quality. A total station was employed to record the location of the resulting forensic evidence, with the collected data analysed using R Studio. The observed patterns suggested that the distribution of remains is fairly consistent in trials under similar environmental conditions. This indicates potential for some general guidelines for forensic evidence collection (for example, the distance from the explosion that a search should cover).

Concepts: Fragment, Distance, Spread Toolkit, BLAST, Explosion

3

Antibody fragments are frequently used as a “crystallization chaperone” to aid structural analysis of complex macromolecules that are otherwise crystallization resistant, but conventional fragment formats have not been designed for this particular application. By fusing an anti-parallel coiled-coil structure derived from the SARAH domain of human Mst1 kinase to the variable region of an antibody, we succeeded in creating a novel chimeric antibody fragment of ∼37 kDa, termed “Fv-clasp,” which exhibits excellent crystallization compatibility while maintaining the binding ability of the original IgG molecule. The “clasp” and the engineered disulfide bond at the bottom of the Fv suppressed the internal mobility of the fragment and shielded hydrophobic residues, likely contributing to the high heat stability and the crystallizability of the Fv-clasp. Finally, Fv-clasp antibodies showed superior “chaperoning” activity over conventional Fab fragments, and facilitated the structure determination of an ectodomain fragment of integrin α6β1.

Concepts: Immune system, Antibody, Protein, Fc receptor, Fragment, Structure, Molecule, Hierarchy