Miracle-dz/UniFAR-FTUs huggingface dataset:
Pitfalls in methods to study colocalization of nanoparticles in mouse macrophage lysosomes

Background In the field of nanoscience there is an increasing interest to follow dynamics of nanoparticles (NP) in cells with an emphasis on endo-lysosomal pathways and long-term NP fate. The accuracy of fluorescence microscopy methods has an important role in obtaining insights into NP interactions with lysosomes at the single cell level including quantification of NP uptake in a specific cell type. During our research on this topic, we encountered several pitfalls, which can bias the experimental outcome. We address some of these pitfalls and suggest possible solutions. Methods Here we use J774A.1 cells as a model for professional phagocytes. We expose them to fluorescently-labelled amorphous silica NP with different sizes and quantify the colocalization of fluorescently-labelled NP with lysosomes over time. We focus on confocal laser scanning microscopy (CLSM), due to its ability to obtain 3D spatial information and follow live cell imaging to study NP colocalization with lysosomes. Results We evaluate different experimental parameters that can bias the colocalization coefficients (i.e, Pearson’s and Manders’), such as the interference of phenol red in the cell culture medium with the fluorescence intensity and image post-processing (effect of spatial resolution, optical slice thickness, pixel saturation and bit depth). Additionally, we determine the correlation coefficients for NP entering the lysosomes under four different experimental set-ups. First, we found out that not only Pearsons’, but also Manders’ correlation coefficient should be considered in lysosome-NP colocalization studies; second, there is a difference in NP colocalization when using NP of different sizes and fluorescence dyes and last, the correlation coefficients might change depending on live-cell and fixed-cell imaging set-up. Conclusions The results summarize detailed steps and recommendations for the experimental design, staining, sample preparation and imaging to improve the reproducibility of colocalization studies between the NP and lysosomes. Graphical Abstract
POTENSI PERDAGANGAN GLOBAL INDONESIA: PENDEKATAN GRAVITY MODEL

In this paper we attempted to estimate trade potential for Indonesia using Gravity model approach. We have used an augmented gravity model to first analyze the Indonesian trade flows and the coefficients thus obtained are then use to predict trade potential for Indonesia. The gravity model has been estimated using OLS technique with cross section data for year 2004. The dependent variables in all our test is total merchandise trade (export plus imports in US dollars), in log form, between pairs of countries. There are two major findings. First, our estimation result show that the gravity equation fits the data and delivers precise and plausible income and distance elasticity. Second, the magnitude of Indonesian’s trade potential is highest with the Asia-pacific region followed by Latin America, Industrial Countries, Central and Eastern Europe, and Sub-Sahara Africa.
Ergenlerde internet bağımlılığını yordayan psiko-sosyal değişkenlerin incelenmesi

Bu arastirmada ergenlerde internet bagimliligini yordayan psiko-sosyal degiskenlerin incelenmesi amaclanmistir. Calismada internet bagimliligini yordayici psiko-sosyal degiskenler olarak yalnizlik, algilanan sosyal destek, yasam doyumu, karsi cinsle romantik iliski durumu, akademik basari ve cinsiyet degiskenleri secilmistir. Arastirmaya 2009-2010 egitim ogretim yilindan Izmir ili Cesme ilcesinde bulunan ortaogretim kurumlarinda 9. , 10. , 11. ve 12.siniflarda ogrenim goren 333’ u kiz, 367’ si erkek 700 ogrenci katilmistir. Arastirmada veri toplama araci olarak Internet Bagimlilik Olcegi, UCLA Yalnizlik Olcegi, Cok Boyutlu Algilanan Sosyal Destek Olcegi, Yasam Doyumu Olcegi ve Kisisel Bilgi Formu kullanilmistir. Arastirmadan elde edilen bulgular incelendiginde, ergenlerde internet bagimliligi ile yalnizlik arasinda pozitif yonde; internet bagimliligi ile aileden algilanan sosyal destek arasinda negatif yonde anlamli bir iliski bulunurken; internet bagimliligi ile cok boyutlu algilanan sosyal destek olceginin alt boyutlarindan olan arkadastan algilanan sosyal destek ve ozel kisiden algilanan sosyal destek arasinda anlamli bir iliski bulunmamistir. Arastirmanin sonucunda cinsiyet, akademik basari, yalnizlik ve aileden algilanan sosyal destek degiskenlerinin ergenlerde internet bagimliligini yordadigi gorulmustur. Soz konusu bu degiskenlerin internet bagimliligindaki toplam varyansin % 7.3’unu aciklamis olmalari nedeniyle internet bagimliligini etkileyen diger degiskenlerin bulunabilmesi icin farkli degiskenleri iceren yeni arastirmalara ihtiyac duyuldugu dusunulmektedir.
The Response of Aboriginal Burning Practices to Population Levels and El Niño–Southern Oscillation Events during the mid- to late-Holocene: a case study from the Sydney Basin using charcoal and pollen analysis

Abstract Pollen and macroscopic charcoal have been analysed from a sedimentary sequence representing approximately 6100 years from a site within Wollemi National Park. This is located to the north-west of Sydney and forms a part of the Greater Blue Mountains World Heritage Area. The overall aim of the work was to examine the prehistoric interrelationships between vegetation, fire and human activity. There were relatively minor changes in the vegetation over the last ∼6000 years, perhaps reflecting the climate- and fire-resilient nature of the sclerophyllous vegetation found on Hawkesbury Sandstone throughout the Sydney Basin. Casuarinaceae declined in the late Holocene, a trend that has been detected in numerous palaeoecological studies throughout south-eastern Australia. This decline was unrelated to fire, which has been a persistent feature at the site over the entire analysed sequence. The fire regime at the site changed from 5.7 ka, which is interpreted as reflecting the onset of increased climatic variability associated with El Niño-Southern Oscillation (ENSO) events. Another dramatic change in the fire regime occurred at 3 ka, which was coeval with archaeological changes in the region. It is possible that the change in fire activity from 3 ka represented an alteration to Aboriginal management strategies associated with an increasing population and/or the increased risk of conflagrations in an ENSO-dominated climate.
The O-methyltransferase SrsB catalyzes the decarboxylative methylation of 5 alkylresorcylic acid during phenolic lipid biosynthesis by Streptomyces griseus 6 7 8

(JB06406-11R) 1 Full-length paper 2 Section: Enzymes and Proteins 3 4 The O-methyltransferase SrsB catalyzes the decarboxylative methylation of 5 alkylresorcylic acid during phenolic lipid biosynthesis by Streptomyces griseus 6 7 8 Chiaki Nakano, Nobutaka Funa, Yasuo Ohnishi*, and Sueharu Horinouchi. 9 10 Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The 11 University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. 12 13 Running title: Decarboxylative methylation of alkylresorcylic acid 14 15 16 *Corresponding author: 17 Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The 18 University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan 19 Tel: +81 3 5841-5123; Fax: +81 3 5841-8021; E-mail: ayasuo@mail.ecc. u-tokyo.ac. jp 20 21 Deceased on 12th July 2009. 22 23 24 25 Copyright © 2012, American Society for Microbiology. All Rights Reserved. J. Bacteriol. doi:10.1128/JB.06406-11 JB Accepts, published online ahead of print on 13 January 2012
Triatoma virus recombinant VP 4 protein induces membrane 2 permeability through dynamic pores

4 5 Rubén Sánchez-Eugenia, Julen Goikolea, David Gil-Cartón, Lissete 6 Sánchez-Magraner, Diego M. A. Guérin 7 8 9 1 Unidad de Biofísica (CSIC, UPV/EHU), Bo Sarriena S/N, 48940 Leioa, 10 Bizkaia, Spain. 11 2 CIC bioGUNE, Structural Biology Unit, Parque Tecnológico Zamudio, 12 48160 Derio, Bizkaia, Spain. 13 3 Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y 14 Tecnología, Universidad del País Vasco (EHU), Bo Sarriena S/N, 48940 15 Leioa, Bizkaia, Spain. 16 17 # Email: diego.guerin@ehu.es 18 19 Running title: TrV VP4 membrane permeability by dynamic pores 20 21 Abstract word count: 201 22 Importance word count: 111 23 Word count: 4957 24 25 JVI Accepted Manuscript Posted Online 11 February 2015 J. Virol. doi:10.1128/JVI.00011-15 Copyright © 2015, American Society for Microbiology. All Rights Reserved.
Ocean cooling: Constraints from changes in Earth's dynamic oblateness (J2) and altimetry

Dynamic oblateness (J2) observations reflect changes in the latitudinal distribution of mass within the Earth system, and hence can give insights into processes involving water transport and sea level rise. We seek to use records of J2 variations deduced from satellite laser ranging, together with altimetry results, to provide an independent geodetic constraint on changes in ocean heat content (OHC). We show that the size and signature of the J2 signal presented here do not support a recently published report of rapid oceanic heat loss beginning in 2003, which was subsequently attributed to Argo and other instrumental bias effects. Our results are consistent with recent findings of a flattening of the OHC trend at this time inferred from the bias‐corrected Argo data, and demonstrate that J2 observations, in combination with other observational and model data types, can provide useful constraints for monitoring and validating ongoing changes in the Earth system.
Nitrates and Angina : an insight into arterial and venular involvment in blood flow regulation

This study t ::sted the hypothesis that venular resistance increases during ischaemia and that a prevalent nitrates-induced venodilatation isthecruc a mechanism underlying their ability to relieveischaemia. Usingthe model of postreactive hyperaemia we used mercuryin-rubber swain gauges to measure forearm blood flow (FBF) and forearm circumference (Fc) before and after 5 mg sublingual isosorbide dinitrate in twelve healthy volunteers. The FC change during reactive hyperaemia was evaluated according to a hydraulic model which assumes that arteriolar resistance (AR) controls the blood inflow and that venular resistance (vR) controls the blood outflow o~: :he vascular capillary reservoir. In this setting FC represents the reservoir volume and any change in this parameter represents the instantaneous difference between input and output flows. In the a3,ence of nitrates and five minutes of arterial closure, the hyperaemic FC curve shows a rapid increase followed by a slow recovery demonstrating a rapid inflow followed by a delayed outflow of the reservoir. This behaviour may be explained by assuming an initial very low arterial resistance and high venular resistance, followed by a slow riequilibrium of the two. Repeati a ~ the experiment after nitrates intake, the hyperaemic Fc curve shows a reduced dimension and a faster recovery to the baseline. (5:mpared with the previous condition, this finding may be explained by assuming a reduced initial venular resistance, which facililates the blood outflow and hence muscle perfusion. Our findings are coherent with an ischaemia-induced arteriolar dilatation,~ hich facilitates filling, and a simultaneous venular constriction which opposes emptying (arteriovenous ischaemic mismat&): the action c: the nitrates seems to restore the mismatch by acting on the venous side. ~a~YWORDS: Reactive hyperaemia, Venous flow, Ischaemia, Nitrates.
Dynamic fluctuations in ascending heart–to–brain modulations under mental stress elicitation

Previous endeavors have revealed how the dynamical information exchange between central and autonomous nervous systems, as measured from brain–heart interplay, can explain emotional arousal and physical stress. In this study, we test our recently proposed computational framework for a functional brain–heart interplay assessment; the Sympatho-Vagal Synthetic Data Generation Model. The model estimates the causal and bidirectional neural modulations between EEG oscillations and sympathetic/parasympathetic activity. Here, mental stress is elicited by increasing the cognitive demand and quantified on 37 human volunteers. The increase on mental stress induced an increased variability on heart–to–brain functional interplay, primarily from sympathetic activity on EEG oscillations in the delta and beta bands. Existing theoretical and experimental evidence has shown that stress involves top-down neural dynamics in the brain. Therefore, our results show that mental stress involves dynamic and bidirectional neural interactions at a brain–body level as well, where bodily feedback shapes the perceived stress caused by an increased cognitive demand. We conclude that brain–heart interplay estimators are suitable biomarkers for stress measurements.
BAI-Net: Individualized Anatomical Cerebral Cartography using Graph Convolutional Network

—Individualized human cerebral cartography has drawn considerable attention in neuroscience research. Many challenges remain, mainly due to large individual variability in brain morphology, connectivity and function. We developed a new tool called brain atlas individualization network (BAI-Net) that automatically parcels individual cerebral cortex into segregated areas using structural and diffusion MRIs. The presented method integrates the group priors into the loss function of graph convolution network, learns the connectivity context of anatomical fingerprints for each area, and consequently provides reliable and explainable individual-specific topography across multiple sessions and different scanners. The BAI-Net model not only captures high variations across individual brains while maintaining high consistency with the priors in the group level, demonstrating high heritability in a twin study, but also shows high associations with behaviors in a cognitive battery. Our method shows high potentials in the field of precision medicine including the diagnosis and treatment of neurological disorders.
Lime-slotting Technique to Ameliorate Subsoil Acidity in a Clay Soil. I. Effects on Soil pH and Physical Characteristics

In soils with subsoil acidity, root growth of plants sensitive to acidity is restricted to surface layers resulting in reduced water and nutrient uptake and low yields of crops. In the present study, the use of the lime-slotting technique, with slots 0.15 m wide and 0.8 m deep, for providing long-term improvements of the adverse soil chemical and physical characteristics of an acid, clay soil was investigated. Lime-slotting using a rotary slotter resulted in a uniform increase in soil pH to the full depth of the slot (0.8 m), indicating a thorough mixing of the lime with the small soil fragments produced by slotting, as they are thrown up into the rotor shroud and redeposited in the slot. In contrast, ripping to 1.0 m depth and delve ploughing to 0.8 m depth only changed the soil pH close to the soil surface. The saturated hydraulic conductivity, total porosity and air-filled porosity at a potential of - 10 kPa measured on soil cores was significantly (P < 0.05) increased within the slot, compared to the undisturbed soil. Values of unsaturated hydraulic conductivities K(e) and diffusivities D(e), calcualted from the saturated conductivity and water potential-water content relationships, also showed increases in the slot, at high water contents. Although a polishing of sections of the slot wall due to rubbing of the rotors was observed in the field, the saturated conductivities of the cores taken across the slot walls did not show significant (P < 0.05) differences compared with the undisturbed soil adjacent to the slot. The extent of protection of the loosened soil in the slots from recompaction during subsequent farm trafficking was evaluated in a vineyard. Soil strength measurement showed distinct differences between field plots which were non-ameliorated, lime-slotted or deep ripped. Soil strength was estimated using penetrometer cone index measurements, which were made when the soils were at similar water contents. Zones of high soil strength observed in the non-ameliorated soils, were reduced in the ripped and slotted soil. However, the upper part of the ripped soil had soil strengths higher than the lower part, indicating repacking under trafficking. In contrast in the slotted soil, the slotted area had low soil strength to depth, indicating greater protection of the loosened soil during trafficking. This could be due to bridging of the tractor wheels and implements across the slot on to the stronger undisturbed soil on either side. Thus, lime-slotting is an effective technique for long-term amelioration of the adverse physical and chemical properties of dense clay soils with subsoil acidity. This should encourage root growth to depth within the slots, and use of the water stored in the subsoil.
Design and Evaluation of CRDMAC: Circular RTR Directional MAC Protocol for WANETs

Using directional antennas in wireless ad hoc networks (WANETs) offers great potential for reducing the radio interference, and improve the communication throughput. Directional antennas, however, introduces new problems in the wireless media access control (MAC), deafness and new hidden terminals, which may cause severe performance degradation. To solve the deafness problem and the new hidden terminal problems, in this paper, we propose an effective Circular RTR Directional MAC (CRDMAC) protocol for WANETs by using a sub-transmission channel and RTR (Ready To Receive) packets, which modifies the IEEE 802.11 distributed coordinated function (DCF). The sub-channel avoids collisions to other ongoing transmission, and the RTR packets notify the neighbor nodes that the mutual transmission has been finished. We evaluate the CRDMAC protocol through simulations. Simulation results show that the proposed protocol outperforms the existing DMAC (Directional MAC) protocol and the CRCM (Circular RTS and CTS MAC) protocol in terms of throughput and packet drop rate.
Intravaginal Practices and Risk of Bacterial Vaginosis and Candidiasis Infection Among a Cohort of Women in the United States

OBJECTIVE: To measure intravaginal practices among women of differing ages, ethnicities, and human immunodeficiency virus status and the association between intravaginal practices and bacterial vaginosis and candidiasis infection. METHODS: Between 2008 and 2010, we recruited and followed sexually active women aged 18–65 years living in Los Angeles. At the enrollment and month 12 visit, participants completed a self-administered, computer-assisted questionnaire covering demographics, sexual behaviors, vaginal symptoms, and intravaginal practices over the past month. At each visit, bacterial vaginosis and candidiasis infection were diagnosed by Nugent criteria and DNA probe, respectively. RESULTS: We enrolled 141 women. Two thirds (66%) reported an intravaginal practice over the past month; 49% reported insertion of an intravaginal product (other than tampons) and 45% reported intravaginal washing. The most commonly reported practices included insertion of commercial sexual lubricants (70%), petroleum jelly (17%), and oils (13%). In univariable analysis, intravaginal use of oils was associated with Candida species colonization (44.4% compared with 5%, P<.01). In multivariable analysis, women reporting intravaginal use of petroleum jelly over the past month were 2.2 times more likely to test positive for bacterial vaginosis (adjusted relative risk 2.2, 95% confidence interval 1.3–3.9). CONCLUSION: Intravaginal insertion of over-the-counter products is common among women in the United States and is associated with increased risk of bacterial vaginosis. The context, motivations for, and effects of intravaginal products and practices on vaginal health are of concern and warrant further study. LEVEL OF EVIDENCE: III
Outcomes of total hip arthroplasty , as a salvage procedure , following failed internal fixation of intracapsular fractures of the femoral neck

s screened for inclusion (n = 24) Records excluded (n = 9) Nature (editorial or letter correspondence) Patient selection Implant selection Full-text articles assessed for eligibility (n = 15) Records excluded (n = 4) Fracture pattern Patient selection Implant selection Full-text articles assessed for eligibility (n = 11) Articles included after references search (n = 0) Studies included in quantitative synthesis (meta-analysis) (n = 5) Studies included in qualitative synthesis (n = 6)
Gestural Control in the English Past-Tense Suffix: An Articulatory Study Using Real-Time MRI

The English past tense allomorph following a coronal stop (e.g., /b ɑ nd ə d/) includes a vocoid that has traditionally been transcribed as a schwa or as a barred i. Previous evidence has suggested that this entity does not involve a specific articulatory gesture of any kind. Rather, its presence may simply result from temporal coordination of the two temporally adjacent coronal gestures, while the interval between those two gestures remains voiced and is acoustically reminiscent of a schwa. The acoustic and articulatory characteristics of this vocoid are reexamined in this work using real-time MRI with synchronized audio which affords complete midsagittal views of the vocal tract. A novel statistical analysis is developed to address the issue of articulatory targetlessness based on previous models that predict articulatory action from segmental context. Results reinforce the idea that this vocoid is different, both acoustically and articulatorily, than lexical schwa, but its targetless nature is not supported. Data suggest that an articulatory target does exist, especially in the pharynx where it is revealed by the new data acquisition methodology. Moreover, substantial articulatory differences are observed between subjects, which highlights both the difficulty in characterizing this entity previously, and the need for further study with additional subjects. constriction in and lower-pharyngeal constriction target
The annual variation of atmospheric CO2 concentration observed in the northern hemisphere

Records of the annual variation of the atmospheric carbon dioxide concentration at Mauna Loa, Point Barrow, and Weathership P are examined for secular changes. The amplitude of the annual variation appears to have increased in recent years with a best estimate of the rate of change, based on the Mauna Loa data, of 0.45 +- 0.42% yr/sup -1/. This change is discussed in terms of changes in biospheric respiration and photosynthesis and the use of fossil fuels. The analysis does not allow for the separation of several possible causes of amplitude change. However, if the change is interpreted as reflecting enhanced biospheric growth, the effect is equivalent to a 8% change in the net summer uptake of carbon over the years 1959-1978 and to a growth of the northern hemisphere seasonal biosphere of 0.5 x 10/sup 12/ kg of carbon per year. Such a conclusion is consistent with recent inventory studies, which indicate that temperature zone forests have acted as a net sink of about 10/sup 12/ kg of carbon per year in recent decades.