bluuebunny/crossref_metadata_2025 huggingface dataset:
Sub‐array partition method based on particle swarm optimisation for large aperture phased array radar
Authors: Chen Xiaoyan , Sun Yuze , Xu Feng , Yang Xiaopeng
Published: July 2019

In order to reduce hardware cost and system complexity, sub‐array partition is necessary for large array antennas. Traditional sub‐array partition methods are mainly aiming at the single performance optimisation of beampattern. Therefore, this study proposes a multiple performance parameters optimisation method based on particle swarm optimisation (PSO). In the proposed method, the multi‐objective optimisation problem is converted into a single‐objective problem, and then dynamic inertia weights and learning factors are used in the algorithm. Based on the proposed method, the signal processing performances can be improved compared with the traditional methods. Through the simulation of the division of the linear array, the effectiveness of the proposed method is verified.
Height estimation improvement via motion compensation based on sub‐aperture method for interferometry SAR system
Authors: Wang Yue , Ma Lixiang , Zhang Fan , Ni Jun , Wu You
Published: July 2019

Baseline is the key factor for highly accuracy terrain elevation measurement in InSAR system. Variation of baseline attitude induced by aircraft's unstable motion leads to phase errors varying along the aperture. The variation will generate prodigious deterioration in DEM's precision. Therefore, in order to reduce the phase errors, critical motion compensation has to be implemented. Here, the sub‐aperture method is introduced to resolve the above issue. The new method is described with mathematical analysis and modelling. The influence of the new method on the sensitivity of roll estimation is also analysed. The simulation and real testing show a very positive result. The roll errors are eliminated greatly in case the sub‐aperture length is optimised. Moreover, the requirements of SNR and azimuth resolution are satisfied.
Endoscopic Endonasal Reconstruction of High-Flow Cerebrospinal Fluid Leak with Fascia Lata “Button” Graft and Nasoseptal Flap: Surgical Technique and Case Series
Authors: Khatiwala Roshni V. , Shastri Karthik S. , Peris-Celda Maria , Kenning Tyler , Pinheiro-Neto Carlos D.
Published: July 2019

Background The endoscopic endonasal approach (EEA) has become increasingly used for resection of skull base tumors in the sellar and suprasellar regions. A nasoseptal flap (NSF) is routinely used for anterior skull base reconstruction; however, there are numerous additional allografts and autografts being used in conjunction with the NSF. The role of perioperative cerebrospinal fluid (CSF) diversion is also unclear.

Objective This study was aimed to analyze success of high-flow CSF leak repair during EEA procedures without use of CSF diversion through lumbar drainage.

Methods A retrospective chart review of patients who had intraoperative high-flow CSF leak during EEA procedures at our institution between January 2013 and December 2017 was performed. CSF leaks were repaired with use of a fascia lata button graft and nasoseptal flap, without use of perioperative lumbar drains.

Results A total of 38 patients were identified (10 male, 28 female). Patient BMIs ranged from 19.7 to 49 kg/m2 (median = 31 kg/m2), with 18 patients meeting criteria for obesity (BMI > 30 kg/m2) and 12 patients overweight (25 kg/m2 < BMI < 29.9 kg/m2). There was no incidence of postoperative CSF leak.

Conclusion In our experience, the nasoseptal flap used in conjunction with the fascia lata button graft is a safe, effective and robust combination for cranial base reconstruction with high-flow intraoperative CSF leaks, without need for lumbar drains.
Patient Outcomes after Reirradiation of Small Skull Base Tumors using Stereotactic Body Radiotherapy, Intensity Modulated Radiotherapy, or Proton Therapy
Authors: Ng Sweet Ping , Wang He , Pollard Courtney , Nguyen Theresa , Bahig Houda , Fuller Clifton D. , Gunn G. Brandon , Garden Adam S. , Reddy Jay P. , Morrison William H. , Shah Shalin , Rosenthal David I. , Frank Steven J. , Guha-Thakurta Nandita , Ferrarotto Renata , Hanna Ehab Y. , Su Shirley Y. , Phan Jack
Published: July 2019

Purpose The aim of this study was to evaluate outcomes of patients who received reirradiation for small skull base tumors utilizing either intensity modulated radiotherapy (IMRT), stereotactic body radiotherapy (SBRT), and proton radiotherapy (PRT).

Methods Patients who received IMRT, SBRT or PRT reirradiation for recurrent or new small skull base tumors (< 60 cc) between April 2000 and July 2016 were identified. Those with < 3 months follow-up were excluded. Clinical outcomes and treatment toxicity were assessed. The Kaplan–Meier method was used to estimate the local control (LC), regional control (RC), distant control (DC), progression free survival (PFS), and overall survival (OS).

Results Of the 75 patients eligible, 30 (40%) received SBRT, 30 (40%) received IMRT, and 15 (20%) received PRT. The median retreatment volume was 28 cc. The median reirradiation dose was 66 Gy in 33 fractions for IMRT/PRT, and 45 Gy in 5 fractions for SBRT. The median time to reirradiation was 41 months. With a median follow-up of 24 months, the LC, RC, DC, PFS, and OS rates were 84%, 79%, 82%, 60%, and 87% at 1 year, and 75%, 72%, 80%, 49%, and 74% at 2 years. There was no difference in OS between radiation modalities. The 1- and 2-year late Grade 3 toxicity rates were 3% and 11% respectively..

Conclusions Reirradiation of small skull base tumors utilizing IMRT, PRT, or SBRT provided good local tumor control and low rates of Grade 3 late toxicity. A prospective clinical trial is needed to guide selection of radiation treatment modalities.
Confined polaronic transport in (LaFeO3)n/(SrFeO3)1 superlattices
Authors: Chang Seo Hyoung , Kim Seong Keun , Kim Young-Min , Dong Yongqi , Folkman Chad M. , Jeong Da Woon , Choi Woo Seok , Borisevich Albina Y. , Eastman Jeffrey A. , Bhattacharya Anand , Fong Dillon D.
Published: July 2019

Functional oxide superlattices offer new and exciting possibilities for the exploration of emergent properties at the nanoscale. While the behavior of La1−xSrxFeO3 films has been extensively investigated at low temperatures, few studies have been carried out at high temperatures, particularly for LaFeO3/SrFeO3 superlattice systems. Here, we investigate the transport behavior and optical properties of (LaFeO3)n/(SrFeO3)1 superlattices at 373 K and above. Using optical spectroscopy, we observe a low energy excitation at ∼1 eV, attributable to charge transfer between the O 2p and Fe 3d states of the δ-doped single SrFeO3 layer. From in-plane conductivity measurements on the superlattices, we determine activation energies that are much lower than those of alloyed samples and vary with the total number of SrFeO3 layers. This suggests that polaronic transport is confined near the SrFeO3 regions, permitting mobilities significantly enhanced over those in alloyed thin films.
Voluntary Wheel Running Attenuates Salt-Induced Vascular Stiffness Independent of Blood Pressure
Authors: Guers John J , Farquhar William B , Edwards David G , Lennon Shannon L
Published: July 2019

BACKGROUND

Excess dietary salt can lead to the development of arterial stiffness and high blood pressure (BP). Regular physical activity can protect against arterial stiffening and lower BP. Less is known regarding the role of exercise on the vasculature independent of BP under high salt (HS) conditions. The aim of the study was to determine whether wheel running protects against the development of dietary salt-induced arterial stiffness independent of BP.

METHODS

Rats were maintained on either normal salt (NS; 0.49% NaCl) or HS (4.0% NaCl) diet for 6 weeks and further divided into a voluntary wheel running (NS-VWR, HS-VWR) or cage control group (NS, HS). Carotid–femoral pulse wave velocity (PWV) was measured using applanation tonometry at baseline (BSL) and 6 weeks.

RESULTS

BP was measured weekly and remained unchanged among groups throughout the 6 weeks (P > 0.05). PWV was elevated at 6 weeks in HS compared to baseline (HS-BSL, 3.27 ± 0.17 vs. HS-6 week, 4.13 ± 0.26 m/s; P < 0.05) and was lower at 6 weeks in both VWR groups (NS-VWR, 2.98 ± 0.29, HS-VWR, 3.11 ± 0.23 m/s) when compared to HS at 6 weeks (P < 0.05). This was supported by a significant increase in aortic collagen I in the HS group alone and transforming growth factor beta (TGF-β) was greater in the HS group compared to both NS groups (P < 0.05). Wheel running resulted in a greater aortic phosphorylated eNOS and SOD-2 in HS-WVR (P < 0.05) compared to HS.

CONCLUSIONS

These data suggest that VWR may protect against collagen accumulation through a TGF-β-mediated pathway by improving nitric oxide bioavailability and redox balance in rats.
Myocardial MMP-2 contributes to SERCA2a proteolysis during cardiac ischaemia–reperfusion injury
Authors: Roczkowsky Andrej , Chan Brandon Y H , Lee Tim Y T , Mahmud Zabed , Hartley Bridgette , Julien Olivier , Armanious Gareth , Young Howard S , Schulz Richard
Published: July 2019

Aims

Matrix metalloproteinase-2 (MMP-2) is a zinc-dependent protease which contributes to cardiac contractile dysfunction when activated during myocardial ischaemia–reperfusion (IR) injury. MMP-2 is localized to several subcellular sites inside cardiac myocytes; however, its role in the sarcoplasmic reticulum (SR) is unknown. The Ca2+ ATPase SERCA2a, which pumps cytosolic Ca2+ into the SR to facilitate muscle relaxation, is degraded in cardiac IR injury; however, the protease responsible for this is unclear. We hypothesized that MMP-2 contributes to cardiac contractile dysfunction by proteolyzing SERCA2a, thereby impairing its activity in IR injury.

Methods and results

Isolated rat hearts were subjected to IR injury in the presence or absence of the selective MMP inhibitor ARP-100, or perfused aerobically as a control. Inhibition of MMP activity with ARP-100 significantly improved the recovery of cardiac mechanical function and prevented the increase of a 70 kDa SERCA2a degradation fragment following IR injury, although 110 kDa SERCA2a and phospholamban levels appeared unchanged. Electrophoresis of IR heart samples followed by LC-MS/MS confirmed the presence of a SERCA2a fragment of ∼70 kDa. MMP-2 activity co-purified with SR-enriched microsomes prepared from the isolated rat hearts. Endogenous SERCA2a in SR-enriched microsomes was proteolyzed to ∼70 kDa products when incubated in vitro with exogenous MMP-2. MMP-2 also cleaved purified porcine SERCA2a in vitro. SERCA activity in SR-enriched microsomes was decreased by IR injury; however, this was not prevented with ARP-100.

Conclusion

This study shows that MMP-2 activity is found in SR-enriched microsomes from heart muscle and that SERCA2a is proteolyzed by MMP-2. The cardioprotective actions of MMP inhibition in myocardial IR injury may include the prevention of SERCA2a degradation.
Aging With Vision Loss: A Framework for Assessing the Impact of Visual Impairment on Older Adults
Authors: Swenor Bonnielin K , Lee Moon J , Varadaraj Varshini , Whitson Heather E , Ramulu Pradeep Y
Published: July 2019

There is limited research examining the impact of visual impairment (VI) on older adults while considering the complexities of aging, leaving gaps in our understanding of how health consequences of VI might be averted. We created a framework integrating concepts from disability, geriatrics, and ophthalmology that conceptualizes how VI challenges successful aging. Here, VI influences multiple functional domains, and increases the risk of negative health outcomes. This model acknowledges that common causes, such as risk factors that affect eyes and other systems simultaneously, may also drive the relationship between VI and health outcomes. Finally, the model highlights how the impact of VI on aging outcomes can be addressed at multiple intervention points.
Diversionary Theory of War
Authors: Jung Sung Chul
Published: July 2019

What causes war? Among others, domestic unrest has been regarded as one of the factors contributing to interstate war. Many scholars, pundits, and policymakers have emphasized internal troubles to account for the occurrence of international wars, including the Falklands War, World Wars I and II, the Russo-Japanese War, and the Imjin War (Japan’s invasion of Korea in the late 16th century). Especially since the end of the Cold War, following the theoretical and methodological suggestions in Levy 1989 (cited under General Overviews), international relations scholars have paid increasingly more attention to domestic unrest and its interaction with other factors such as regime type and strategic rivalry to explain interstate and intrastate conflict. By taking different methodologies, such as quantitative statistical analysis, in-depth case study, and formal modeling, they build causal processes linking domestic unrest to international conflict, identify various factors at the levels of the individual, state, and dyad affecting the onset of a diversionary conflict, and provide empirical evidence supporting or disproving their theories.
Artificial Discretion as a Tool of Governance: A Framework for Understanding the Impact of Artificial Intelligence on Public Administration
Authors: Young Matthew M , Bullock Justin B , Lecy Jesse D
Published: July 2019

Public administration research has documented a shift in the locus of discretion away from street-level bureaucrats to “systems-level bureaucracies” as a result of new information communication technologies that automate bureaucratic processes, and thus shape access to resources and decisions around enforcement and punishment. Advances in artificial intelligence (AI) are accelerating these trends, potentially altering discretion in public management in exciting and in challenging ways. We introduce the concept of “artificial discretion” as a theoretical framework to help public managers consider the impact of AI as they face decisions about whether and how to implement it. We operationalize discretion as the execution of tasks that require nontrivial decisions. Using Salamon’s tools of governance framework, we compare artificial discretion to human discretion as task specificity and environmental complexity vary. We evaluate artificial discretion with the criteria of effectiveness, efficiency, equity, manageability, and political feasibility. Our analysis suggests three principal ways that artificial discretion can improve administrative discretion at the task level: (1) increasing scalability, (2) decreasing cost, and (3) improving quality. At the same time, artificial discretion raises serious concerns with respect to equity, manageability, and political feasibility.
Learning, Fast or Slow
Authors: Barber Brad M , Lee Yi-Tsung , Liu Yu-Jane , Odean Terrance , Zhang Ke
Published: July 2019

Rational models claim “trading to learn” explains widespread excessive speculative trading and challenge behavioral explanations of excessive trading. We argue rational learning models do not explain speculative trading by studying day traders in Taiwan. Consistent with previous studies of learning, unprofitable day traders are more likely than profitable traders to quit. Consistent with models of overconfidence and biased learning (but not with rational learning), the aggregate performance of day traders is negative; 74% of day trading volume is generated by traders with a history of losses; and 97% of day traders are likely to lose money in future day trading.

Received: March 4, 2019; Editorial decision: May 16, 2019 by Editor: Jeffrey Pontiff. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Role of Mouse Cytochrome P450 Enzymes of the Cyp2abfgs Subfamilies in the Induction of Lung Inflammation by Cigarette Smoke Exposure
Authors: Hartog Matthew , Zhang Qing-Yu , Ding Xinxin
Published: July 2019

Many constituents of tobacco smoke (TS) require bioactivation to exert toxic effects; however, few studies have examined the role of bioactivation enzymes in the adverse effects of TS exposure. This knowledge gap is a major source of uncertainty for risk assessment and chemoprevention efforts. Our aim is to test the hypothesis that cytochrome P450 (P450) enzyme-mediated bioactivation is essential to the development of TS exposure-induced lung toxicity, by determining the contributions of P450 enzymes in the mouse Cyp2abfgs gene subfamilies to environmental tobacco smoke (ETS)-induced lung inflammation. Adult female wildtype (WT) and Cyp2abfgs-null mice (both on C57BL/6J background) were exposed to filtered air or ETS, intermittently, for 1 or 2 weeks. Lung inflammation was assessed by quantification of inflammatory cells, cytokines, chemokines, and proteins in bronchoalveolar lavage fluid (BALF) and histopathological analysis. Glutathione (GSH) conjugates of 2 ETS constituents, naphthalene (NA), and 3-methylindole (3MI), were measured in mice exposed to ETS for 4 h. Persistent macrophagic and neutrophilic lung inflammation was observed in ETS-exposed WT mice; the extent of which was significantly reduced in ETS-exposed Cyp2abfgs-null mice. Levels of proinflammatory cytokines and chemokines, along with the total protein concentration, were increased in cell-free BALF from ETS-exposed WT mice, but not Cyp2abfgs-null mice. Additionally, GSH conjugates of NA and 3MI were detected in the lungs of WT, but not Cyp2abfgs-null, mice following ETS exposure. These results provide the first in vivo evidence that the mouse Cyp2abfgs gene cluster plays an important role in ETS-induced lung inflammation.
A synthetic approach for assessing the interplay of form and function in the crocodyliform snout
Authors: Drumheller Stephanie K , Wilberg Eric W
Published: July 2019

Existing classifications of snout shape within Crocodylia are supported by functional studies, but ecological surveys often reveal a higher than expected diversity of prey items within putatively specialist groups, and research into bite force and predation behaviour does not always reveal significant differences between snout shape groups. The addition of more distantly related crocodyliforms complicates the ecomorphological signal, because these groups often occupy a larger area of morphospace than the crown group alone. Here, we present an expanded classification of snout shapes and diets across Crocodyliformes, bringing together geometric morphometrics, non-hierarchical cluster analyses, phylogenetic analyses, ancestral state reconstructions, ecological surveys of diet, and feeding traces from the fossil record to build and test predictive models for linking snout shape and function across the clade. When applied to living members of the group, these new classifications partition out based on differences in predator body mass and maximal prey size. When applied to fossils, these classifications predict potential prey items and identify possible examples of scavenging. In a phylogenetic context, these ecomorphs reveal differences in dietary strategies and diversity within major crocodyliform clades. Taken together, these patterns suggest that crocodyliform diversity, in terms of both morphology and diet, has been underestimated.
IL‐6/p‐BTK/p‐ERK signaling mediates calcium phosphate‐induced pruritus
Authors: Keshari Sunita , Sipayung Apriska Dewi , Hsieh Ching‐Chuan , Su Li‐Jen , Chiang Yun‐Ru , Chang Huan‐Cheng , Yang Wu‐Chang , Chuang Tsung‐Hsien , Chen Chien‐Lung , Huang Chun‐Ming
Published: July 2019

Uremic pruritus with elevated levels of calcium phosphate (CaP) in skin is a common symptom in patients with chronic kidney disease (CKD). In this study, we demonstrate that intradermal injection of CaP into mice triggered scratching by up‐regulating the IL‐6 in skin and phosphorylation of ERKs in dorsal root ganglion (DRG) in a dose‐dependent manner. IL‐6 is essential because the CaP‐induced up‐regulation of phosphorylated (p)‐ERK in DRG was considerably reduced in the IL‐6 knockout mice. Microarray analysis in conjunction with real‐time PCR revealed a higher mRNA expression of Bruton's tyrosine kinase (BTK) gene in DRG after CaP injection. The inhibition of BTK by ibrutinib noticeably diminish the CaP‐induced up‐regulation of IL‐6 and p‐ERK in mice. A high amount of IL‐6 was detected in itchy skin and blood of patients with CKD. The expressions of p‐BTK and p‐ERK in DRG primary cells reached maximum levels at 1 and 10 min, respectively, after treatment of recombinant IL‐6 and were significantly reduced by treatment of IL‐6 along with ibrutinib. The mechanism by which the CaP‐induced pruritus mediated by the IL‐6/p‐BTK/p‐ERK signaling was revealed.—Keshari, S., Sipayung, A. D., Hsieh, C.‐C., Su, L.‐J., Chiang, Y.‐R., Chang, H.‐C., Yang, W.‐C., Chuang, T.‐H., Chen, C.‐L., Huang, C.‐M. IL‐6/p‐BTK/p‐ERK signaling mediates calcium phosphate‐induced pruritus. FASEB J. 33, 12036‐12046 (2019). www.fasebj.org
EXPRESSION OF CONCERN: Mitophagy protects against statin‐mediated skeletal muscle toxicity
Authors: Ramesh idula , Campos Juliane C. , Lee Pamela , Song Yang , Hernandez Genaro , Sin Jon , Tucker Kyle C. , Saadaeijahromi Hannaneh , Gurney Michael , Ferreira Julio C. B. , Andres Allen M.
Published: July 2019

The deleterious effects of statins on skeletal muscle are well known, but the mechanism associated with these effects remains unresolved. Statins are associated with mitochondrial damage, which may contribute to muscle myopathy. Here we demonstrate that simvastatin induces mitophagy in skeletal muscle cells and hypothesized that attenuating this process by silencing the mitophagy adapter p62/sequestosome‐1 (SQSTM1) might mitigate myotoxicity. Surprisingly, silencing p62/SQSTM1 in differentiated C2C12 muscle cells exacerbated rather than attenuated myotoxicity. This inhibition of mitophagy in the face of statin challenge correlated with increased release of cytochrome c to the cytosol, activation of caspase‐3, and lactate dehydrogenase (LDH) release. Correspondingly, targeted knockdown of Parkin, a canonical E3 ubiquitin ligase important for mitophagy, mirrored the effects of p62/SQSTM1 silencing. To corroborate these findings in vivo, we treated Parkin knockout mice with simvastatin for 2 wk. In line with our findings in vitro, these mitophagy‐compromised mice displayed reduced spontaneous activity, loss of grip strength, and increased circulating levels of muscle damage marker LDH. Our findings demonstrate that mitophagy is an important mechanism to resist statin‐induced skeletal muscle damage.—Ramesh, M., Campos, J. C., Lee, P., Song, Y., Hernandez, G., Sin, J., Tucker, K. C., Saadaeijahromi, H., Gurney, M., Ferreira, J. C. B., Andres, A. M. Mitophagy protects against statin‐mediated skeletal muscle toxicity. FASEB J. 33, 11857‐11869 (2019). www.fasebj.org
Inequality in resource allocation and population dynamics models
Authors: Anazawa Masahiro
Published: July 2019

The Hassell model has been widely used as a general discrete-time population dynamics model that describes both contest and scramble intraspecific competition through a tunable exponent. Since the two types of competition generally lead to different degrees of inequality in the resource distribution among individuals, the exponent is expected to be related to this inequality. However, among various first-principles derivations of this model, none is consistent with this expectation. This paper explores whether a Hassell model with an exponent related to inequality in resource allocation can be derived from first principles. Indeed, such a Hassell model can be derived by assuming random competition for resources among the individuals wherein each individual can obtain only a fixed amount of resources at a time. Changing the size of the resource unit alters the degree of inequality, and the exponent changes accordingly. As expected, the Beverton–Holt and Ricker models can be regarded as the highest and lowest inequality cases of the derived Hassell model, respectively. Two additional Hassell models are derived under some modified assumptions.
Early animal evolution: a morphologist's view
Authors: Nielsen Claus
Published: July 2019

Two hypotheses for the early radiation of the metazoans are vividly discussed in recent phylogenomic studies, the ‘Porifera-first’ hypothesis, which places the poriferans as the sister group of all other metazoans, and the ‘Ctenophora-first’ hypothesis, which places the ctenophores as the sister group to all other metazoans. It has been suggested that an analysis of morphological characters (including specific molecules) could throw additional light on the controversy, and this is the aim of this paper. Both hypotheses imply independent evolution of nervous systems in Planulozoa and Ctenophora. The Porifera-first hypothesis implies no homoplasies or losses of major characters. The Ctenophora-first hypothesis shows no important synapomorphies of Porifera, Planulozoa and Placozoa. It implies either independent evolution, in Planulozoa and Ctenophora, of a new digestive system with a gut with extracellular digestion, which enables feeding on larger organisms, or the subsequent loss of this new gut in the Poriferans (and the re-evolution of the collar complex). The major losses implied in the Ctenophora-first theory show absolutely no adaptational advantages. Thus, morphology gives very strong support for the Porifera-first hypothesis.
Reverse vaccinology and subtractive genomics reveal new therapeutic targets againstMycoplasma pneumoniae: a causative agent of pneumonia
Authors: Vilela Rodrigues Thaís Cristina , Jaiswal Arun Kumar , de Sarom Alissa , de Castro Oliveira Letícia , Freire Oliveira Carlo José , Ghosh Preetam , Tiwari Sandeep , Miranda Fábio Malcher , de Jesus Benevides Leandro , Ariston de Carvalho Azevedo Vasco , de Castro Soares Siomar
Published: July 2019

Pneumonia is an infectious disease caused by bacteria, viruses or fungi that results in millions of deaths globally. Despite the existence of prophylactic methods against some of the major pathogens of the disease, there is no efficient prophylaxis against atypical agents such asMycoplasma pneumoniae, a bacterium associated with cases of community-acquired pneumonia. Because of the morphological peculiarity ofM. pneumoniae, which leads to an increased resistance to antibiotics, studies that prospectively investigate the development of vaccines and drug targets appear to be one of the best ways forward. Hence, in this paper, bioinformatics tools were used for vaccine and pharmacological prediction. We conducted comparative genomic analysis on the genomes of 88M. pneumoniaestrains, as opposed to a reverse vaccinology analysis, in relation to the capacity ofM. pneumoniaeproteins to bind to the major histocompatibility complex, revealing seven targets with immunogenic potential. Predictive cytoplasmic proteins were tested as potential drug targets by studying their structures in relation to other proteins, metabolic pathways and molecular anchorage, which identified five possible drug targets. These findings are a valuable addition to the development of vaccines and the selection of newin vivodrug targets that may contribute to further elucidating the molecular basis ofM. pneumoniae–host interactions.
Three-dimensionally preserved soft tissues and calcareous hexactins in a Silurian sponge: implications for early sponge evolution
Authors: Nadhira Ardianty , Sutton Mark D. , Botting Joseph P. , Muir Lucy A. , Gueriau Pierre , King Andrew , Briggs Derek E. G. , Siveter David J. , Siveter Derek J.
Published: July 2019

Sponges (Porifera), as one of the earliest-branching animal phyla, are crucial for understanding early metazoan phylogeny. Recent studies of Lower Palaeozoic sponges have revealed a variety of character states and combinations unknown in extant taxa, challenging our views of early sponge morphology. The Herefordshire Konservat–Lagerstätte yields an abundant, diverse sponge fauna with three-dimensional preservation of spicules and soft tissue.
Carduispongia pedicula
gen. et sp. nov. possesses a single layer of hexactine spicules arranged in a regular orthogonal network. This spicule type and arrangement is characteristic of the reticulosans, which have traditionally been interpreted as early members of the extant siliceous Class Hexactinellida. However, the unusual preservation of the spicules of
C
.
pedicula
reveals an originally calcareous composition, which would be diagnostic of the living Class Calcarea. The soft tissue architecture closely resembles the complex sylleibid or leuconid structure seen in some modern calcareans and homoscleromorphs. This combination of features strongly supports a skeletal continuum between primitive calcareans and hexactinellid siliceans, indicating that the last common ancestor of Porifera was a spiculate, solitary, vasiform animal with a thin skeletal wall.
Common latitudinal gradients in functional richness and functional evenness across marine and terrestrial systems
Authors: Schumm M. , Edie S. M. , Collins K. S. , Gómez-Bahamón V. , Supriya K. , White A. E. , Price T. D. , Jablonski D.
Published: July 2019

Functional diversity is an important aspect of biodiversity, but its relationship to species diversity in time and space is poorly understood. Here we compare spatial patterns of functional and taxonomic diversity across marine and terrestrial systems to identify commonalities in their respective ecological and evolutionary drivers. We placed species-level ecological traits into comparable multi-dimensional frameworks for two model systems, marine bivalves and terrestrial birds, and used global species-occurrence data to examine the distribution of functional diversity with latitude and longitude. In both systems, tropical faunas show high total functional richness (FR) but low functional evenness (FE) (i.e. the tropics contain a highly skewed distribution of species among functional groups). Functional groups that persist toward the poles become more uniform in species richness, such that FR declines and FE rises with latitude in both systems. Temperate assemblages are more functionally even than tropical assemblages subsampled to temperate levels of species richness, suggesting that high species richness in the tropics reflects a high degree of ecological specialization within a few functional groups and/or factors that favour high recent speciation or reduced extinction rates in those groups.
Backtracking during navigation is correlated with enhanced anterior cingulate activity and suppression of alpha oscillations and the ‘default-mode’ network
Authors: Javadi Amir-Homayoun , Patai Eva Zita , Marin-Garcia Eugenia , Margois Aaron , Tan Heng-Ru M. , Kumaran Dharshan , Nardini Marko , Penny Will , Duzel Emrah , Dayan Peter , Spiers Hugo J.
Published: July 2019

Successful navigation can require realizing the current path choice was a mistake and the best strategy is to retreat along the recent path: ‘back-track’. Despite the wealth of studies on the neural correlates of navigation little is known about backtracking. To explore the neural underpinnings of backtracking we tested humans during functional magnetic resonance imaging on their ability to navigate to a set of goal locations in a virtual desert island riven by lava which constrained the paths that could be taken. We found that on a subset of trials, participants spontaneously chose to backtrack and that the majority of these choices were optimal. During backtracking, activity increased in frontal regions and the dorsal anterior cingulate cortex, while activity was suppressed in regions associated with the core default-mode network. Using the same task, magnetoencephalography and a separate group of participants, we found that power in the alpha band was significantly decreased immediately prior to such backtracking events. These results highlight the importance for navigation of brain networks previously identified in processing internally-generated errors and that such error-detection responses may involve shifting the brain from default-mode states to aid successful spatial orientation.
The biggest losers: habitat isolation deconstructs complex food webs from top to bottom
Authors: Ryser Remo , Häussler Johanna , Stark Markus , Brose Ulrich , Rall Björn C. , Guill Christian
Published: July 2019

Habitat fragmentation threatens global biodiversity. To date, there is only limited understanding of how the different aspects of habitat fragmentation (habitat loss, number of fragments and isolation) affect species diversity within complex ecological networks such as food webs. Here, we present a dynamic and spatially explicit food web model which integrates complex food web dynamics at the local scale and species-specific dispersal dynamics at the landscape scale, allowing us to study the interplay of local and spatial processes in metacommunities. We here explore how the number of habitat patches, i.e. the number of fragments, and an increase of habitat isolation affect the species diversity patterns of complex food webs (α-,β-,γ-diversities). We specifically test whether there is a trophic dependency in the effect of these two factors on species diversity. In our model, habitat isolation is the main driver causing species loss and diversity decline. Our results emphasize that large-bodied consumer species at high trophic positions go extinct faster than smaller species at lower trophic levels, despite being superior dispersers that connect fragmented landscapes better. We attribute the loss of top species to a combined effect of higher biomass loss during dispersal with increasing habitat isolation in general, and the associated energy limitation in highly fragmented landscapes, preventing higher trophic levels to persist. To maintain trophic-complex and species-rich communities calls for effective conservation planning which considers the interdependence of trophic and spatial dynamics as well as the spatial context of a landscape and its energy availability.
Quality characteristics of grapes stored using phytoncide and sulfur dioxide pads
Authors: Jeon Ki-Hong , Choi Jin-Young , Kim Bae-Yong , Memon Azra , Lee Woon-Kyu
Published: July 2019

In order to study the shelf life of grapes, appearance, weight loss, shattering rate, pH, titratable acidity, sugar content, color, free sugar, organic acid, and ethanol contents of grapes grown in were measured for 12 days of storage at room temperature by treatments with phytoncide pads derived from pine tree (phytoncide pad 1 and phytoncide pad 2) and a sulfur dioxide pad as well as a control group with pad only. As the storage period increased, the color of the sulfur dioxide pad changed to red. The weight reduction rate significantly increased by the sulfur dioxide pad treatment and the lowest weight reduction rate was obtained by the phytoncide 2 treatment. The percentage of the highest shattering rate was determined on the 12th day of storage in the control. Moreover, the sulfur dioxide pad treatment was carried out at the lowest pH, and the phytoncide 2 treatment at the highest pH. Titratable acidity increased until the 6th day of storage, but decreased at the 12th day for both treatments. The sugar content decreased with increasing storage period, and the control group showed the highest decrease with 13.13-13.50 °Brix on the 12th storage day. The L and a value were increased in the sulfur dioxide pad treatment, and the b value increased in all treatments except the phytoncide pad 2 treatment at the 12th day of storage. Fructose content was 56,805.88-67,157.12 mg/L on the 12th day of storage. In the phytoncide pad 1 treatment, it showed a low decrease in fructose content during the storage period. A similar decrease in the content of tartaric acid, which is the highest content in the organic acids of grapes, was observed in all treatments except in the control. The lowest increase in ethanol content was observed in the phytoncide pad 2 treatment during the storage period. Therefore, grapes were better preserved by the phytoncide pad 2 treatment at room temperature than that by using conventional sulfite pads.
The quality, antioxidant activity, and storage behavior of milk fermented with Ligularia fischeri extracts
Authors: Cho Ja-Yong , Jeong Jae-Hee , Park Sang-Jun , Na Ji-Hoon , Lee Cheol-Gyo , Cho In-Kyung , Huh Chang-Ki , Kim Yong-Doo
Published: July 2019

In this study, milk samples were fermented following the addition of Ligularia fischeri extracts. The aqueous extracts were obtained from L. fischer grown in the open field (OL) or in a greenhouse (GL). The quality related properties, and antioxidant activity of the fermented milk were evaluated, and the effects of storage on the fermented samples were assessed. The time required for the fermented milk to reach pH 4.6 was approximately four hours in all samples. The titratable acidity of the samples was in the range of 0.5-1%. The number of lactic acid bacteria in the fermented milks made with L. fischeri GL extract was slightly higher than it was in milks samples fermented with L. fischeri OL extract. The Hunter Lab color (L) and redness (a) values of the samples were lower after fermentation, but their yellowness (b) increased with increasing amounts of L. fischeri extracts. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity in milk fermented with 0.5%, 1%, 3%, and 8% L. fischeri OL extracts was higher than that in milk fermented with corresponding amounts of L. fischeri GL extract. However, the difference was not significant. DPPH activity in milk fermented with 5% L. fischeri GL extract was higher than it was in milk fermented with 5% L. fischeri OL extract. The pattern of 2,2’-azinobis-(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS˙+) scavenging activity in the samples was similar to that observed during the DPPH assay. The pH and, titratable acidity, of the fermented samples were not significantly affected by storage, and the number of lactic acid bacteria in the stored and freshly fermented samples was similar.
Determinaton of physiological ripening time based on change in physicochemical characteristics during fruit development of ‘Hanareum’ pear (P. pyrifolia Nakai)
Authors: Kim Yoon-Kyeong , Won KyungHo , Lee In Bog , Lee ByulHaNa , Lee Ug-Yong , Kang Sam-Seok , Shin Il-Sheob , Jeong Hae Won
Published: July 2019

This study was conducted to determine the optimal physiological ripening time and suggest a reasonable harvest time indicator by analyzing the relationship between change in physicochemical characteristics and the sugar composition change patterns during development of 'Hanareum' fruit from 54 days after full bloom (DAFB) to 130 DAFB. The weight of fruits from 96 to 115 DAFB rapidly increased and then became gentle showing a typical sigmoidal curve. Flesh hardness decreased steadily after 96 DAFB; there was no significant difference in flesh hardness for 115, 125 and 130 DAFB fruits. The starch content began to reduce around the core for 119 DAFB. Moreover, sucrose and fructose contents started to increase with fruit development; however, the sucrose content continuously increased, whereas the fructose content started to decrease for 110 DAFB. Fruits of 125 and 130 DAFB did not show coloration according to the iodine test. Based on these results, it was estimated that the optimal physiological ripening time of 'Hanareum' was between 119 and 125 DAFB. The results of correlation analysis between fruit development change and sugar composition change patterns of fruits of 'Hanareum' showed that there was a strong linear relationship. Correlation coefficient between the sucrose/fructose (S/F) ratio and flesh hardness is -0.57, between S/F ratio and iodine test results is 0.80. Namely, S/F ratio is possible to use for harvest time determination indicator and the point of S/F ratio of 0.9–1.1 was considered to be ideal for the determination of the optimal physiological ripening time at which starch completely degrades.
Optimal enzymatic hydrolysis conditions for increased production of L-arginine and GABA in Dendropanax morbifera Lev. leaves
Authors: Lee Ki Hoon , Kim Sunoh
Published: July 2019

Dendropanax morbifera Lev. (DP) leaves have the potential for use as a functional food ingredient. In this study, D. morbifera Lev. leaves were subjected to enzymatic hydrolysis by proteinase, peptidase, trypsin, bromelain, and papain to increase L-arginine and γ-aminobutyric acid (GABA) levels. Hydrolysis time, temperature, pH, vacuum conditions, enzyme type, enzyme concentration, and the order of enzyme administration were optimized to increase L-arginine and GABA concentrations. L-arginine and GABA recoveries were higher when enzymatic treatment was performed prior to the extraction process. No significant changes in L-arginine and GABA production were observed with changes in pH, vacuum conditions, or enzyme concentration. The optimized procedure for obtaining the highest L-arginine and GABA concentrations was to inactivate the enzymes after 8 h of hydrolysis, extract the leaves, and to perform a second hydrolysis step at 16 h with proteinase, trypsin, bromelain, and papain. By increasing L-arginine and GABA levels simultaneously, high-quality hydrolyzed D. morbifera Lev. extract (Hy-DP) was produced efficiently in large quantities at a low cost. With this enzymatic treatment and extraction process, Hy-DP has the potential for use as a functional food ingredient. Further evaluation of Hy-DP as a functional food additive may allow it to be used in foods.
Exfoliated near infrared fluorescent CaCuSi4O10 nanosheets with ultra-high photostability and brightness for biological imaging
Authors: Selvaggio Gabriele , Preiß Helen , Chizhik Alexey , Nißler Robert , Mann Florian A. , Lv Zhiyi , Oswald Tabea A. , Spreinat Alexander , Erpenbeck Luise , Großhans Jörg , Giraldo Juan Pablo , Kruss Sebastian
Published: July 2019

Imaging of complex (biological) samples in the near infrared (nIR) range of the spectrum is beneficial due to reduced light scattering, absorption, phototoxicity and autofluorescence. However, there are only few near infrared fluorescent materials known and suitable for biomedical applications. Here, we exfoliate the layered pigment CaCuSi4O10 (known as Egyptian Blue, EB) via facile tip sonication into nanosheets (EB-NS) with ultra-high nIR fluorescence stability and brightness. The size of EB-NS can be tailored by tip sonication to diameters < 20 nm and heights down to 1 nm. EB-NS fluoresce at 910 nm and the total fluorescence intensity scales with the number of Cu2+ ions that serve as luminescent centers. Furthermore, EB-NS display no bleaching and ultra-high brightness compared to other nIR fluorophores. The versatility of EB-NS is demonstrated by in vivo single-particle tracking and microrheology measurements in developing Drosophila embryos. Additionally, we show that EB-NS can be uptaken by plants and remotely detected in a low cost stand-off detection setup despite strong plant background fluorescence. In summary, EB-NS are a highly versatile, bright, photostable and biocompatible nIR fluorescent material that has the potential for a wide range of bioimaging applications both in animal and plant systems.
Cell cycle variants duringDrosophilaaccessory gland development
Authors: Box Allison M. , Ramesh Navyashree A. , Nandakumar Shyama , Church Samuel Jaimian , Prasad Dilan , Afrakhteh Ariana , Taichman Russell S. , Buttitta Laura
Published: July 2019

TheDrosophila melanogasteraccessory gland is a functional analog of the mammalian prostate containing two secretory epithelial cell types, termed main and secondary cells. This tissue is responsible for making and secreting seminal fluid proteins and other molecules that contribute to successful reproduction. The cells of this tissue are bi-nucleate and polyploid, due to variant cell cycles that include endomitosis and endocycling during metamorphosis. Here we provide evidence of additional cell cycle variants in this tissue. We show that main cells of the gland are connected by ring canals that form after the penultimate mitosis and we describe an additional post-eclosion endocycle required for gland maturation that is dependent on juvenile hormone signaling. We present evidence that the main cells of theDrosophila melanogasteraccessory gland undergo a unique cell cycle reprogramming throughout organ development that results in step-wise cell cycle truncations culminating in cells containing two octoploid nuclei with under-replicated heterochromatin in the mature gland. We propose this tissue as a model to study developmental and hormonal temporal control of cell cycle variants in terminally differentiating tissues.
Physical factors contributing to regulation of bacterial surface motility
Authors: Rhodeland Ben , Hoeger Kentaro , Ursell Tristan
Published: July 2019

Microbes routinely face the challenge of acquiring territory and resources on wet surfaces. Cells move in large groups inside thin, surface-bound water layers, often achieving speeds of 30 µm/s within this environment, where viscous forces dominate over inertial forces (low Reynolds number). The canonical Gram-positive bacterium Bacillus subtilis is a model organism for the study of collective migration over surfaces with groups exhibiting motility on length scales three orders of magnitude larger than themselves within a few doubling times. Genetic and chemical studies clearly show that the secretion of endogenous surfactants and availability of free surface water are required for this fast group motility. Here we show that: (i) water availability is a sensitive control parameter modulating an abiotic jamming-like transition that determines whether the group remains fluidized and therefore collectively motile, (ii) groups self-organize into discrete layers as they travel, (iii) group motility does not require proliferation, rather groups are pulled from the front, and (iv) flow within expanding groups is capable of moving material from the parent colony into the expanding tip of a cellular dendrite with implications for expansion into regions of varying nutrient content. Together, these findings illuminate the physical structure of surface-motile groups and demonstrate that physical properties, like cellular packing fraction and flow, regulate motion from the scale of individual cells up to length scales of centimeters.
Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines
Authors: Dempster Joshua M. , Rossen Jordan , Kazachkova Mariya , Pan Joshua , Kugener Guillaume , Root David E. , Tsherniak Aviad
Published: July 2019

One of the main goals of the Cancer Dependency Map project is to systematically identify cancer vulnerabilities across cancer types to accelerate therapeutic discovery. Project Achilles serves this goal through the in vitro study of genetic dependencies in cancer cell lines using CRISPR/Cas9 (and, previously, RNAi) loss-of-function screens. The project is committed to the public release of its experimental results quarterly on the DepMap Portal (https://depmap.org), on a pre-publication basis. As the experiment has evolved, data processing procedures have changed. Here we present the current and projected Achilles processing pipeline, including recent improvements and the analyses that led us to adopt them, spanning data releases from early 2018 to the first quarter of 2020. Notable changes include quality control metrics, calculation of probabilities of dependency, and correction for screen quality and other biases. Developing and improving methods for extracting biologically-meaningful scores from Achilles experiments is an ongoing process, and we will continue to evaluate and revise data processing procedures to produce the best results.