Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting neo‐adjuvant chemotherapy response and progression‐free survival of locally advanced breast cancer using textural features of intratumoral heterogeneity on F‐18 FDG PET/CT and diffusion‐weighted MR imaging

Predicting response to neo‐adjuvant chemotherapy (NAC) and survival in locally advanced breast cancer (LABC) is important. This study investigated the prognostic value of tumor heterogeneity evaluated with textural analysis through F‐18 fluorodeoxyglucose (FDG) positron emission tomography (PET) and diffusion‐weighted imaging (DWI). We enrolled 83 patients with LABC who had completed NAC and curative surgery. Tumor texture indices from pretreatment FDG PET and DWI were extracted from histogram analysis and 7 different parent matrices: co‐occurrence matrix, the voxel‐alignment matrix, neighborhood intensity difference matrix, intensity size‐zone matrix (ISZM), normalized gray‐level co‐occurrence matrix (NGLCM), neighboring gray‐level dependence matrix (NGLDM), and texture spectrum matrix. The predictive values of textural features were tested regarding both pathologic NAC response and progression‐free survival. Among 83 patients, 46 were pathologic responders, while 37 were nonresponders. The PET texture indices from 7 parent matrices, DWI texture indices from histogram, and 1 parent matrix (NGLCM) showed significant differences according to NAC response. On multivariable analysis, number nonuniformity of PET extracted from the NGLDM was an independent predictor of pathologic response (P = .009). During a median follow‐up period of 17.3 months, 14 patients experienced recurrence. High‐intensity zone emphasis (HIZE) and high‐intensity short‐zone emphasis (HISZE) from PET extracted from ISZM were significant textural predictors (P = .011 and P = .033). On Cox regression analysis, only HIZE was a significant predictor of recurrence (P = .027), while HISZE showed borderline significance (P = .107). Tumor texture indices are useful for NAC response prediction in LABC. Moreover, PET texture indices can help to predict disease recurrence.
Land use change and pollinator extinction debt in exurban landscapes

For the first time in more than a century, people across the planet are migrating en mass from cities to rural areas. In this process of ‘exurbanisation’ humans are rapidly converting natural and agricultural regions into low‐density housing. Despite the scale of this exurban development and its potential negative impact on biodiversity, little is known about how this specific type of land conversion impacts wild pollinators. In this study, we conduct an extensive survey of the wild pollinators of the peach agroecosystem and investigate the impact of current and historic land use at multiple spatial scales on pollinator community composition within agroecological landscapes that have recently undergone exurban development. We reveal that the overall composition of the wild pollinator community is significantly associated with current local agricultural and natural land cover. Specifically, local agricultural land use was associated with ground‐nesting bee community composition, whereas natural lands were associated with cavity‐nesting bee composition, revealing that nesting materials drive community composition for these two groups in exurban habitats. In contrast, community composition for butterflies and flies, which made up the smallest proportion of our communities, were not strongly associated with any particular land use type, likely due to their non‐central place foraging strategy. Most interestingly, our results indicate that historic land use remains a significant factor impacting the current abundance of all pollinators in the peach agroecosystem, offering the first evidence of extinction debt in this rapidly expanding exurban landscape.
Adiponectin is present in human milk and is associated with maternal factors.

BACKGROUND Previous studies have shown that human milk has a role in the gastrointestinal, neural, and immune development of neonates. If present in milk, adiponectin would be a promising candidate for influencing infant development, given its metabolic functions. OBJECTIVES Our objectives were to determine whether adiponectin is present in human milk and to characterize maternal factors associated with potential variation in milk adiponectin concentrations. DESIGN We quantified adiponectin concentrations in human milk samples from donors to the Cincinnati Children's Research Human Milk Bank and randomly selected participants in a cohort study in Mexico City funded by the National Institutes of Health. Using cross-sectional and longitudinal data, we examined milk adiponectin concentrations in relation to lactation duration, maternal body mass index (BMI; in kg/m(2)), and ethnicity. RESULTS Adiponectin was detected in human skim milk (range: 4.2-87.9 ng/mL). In cross-sectional and longitudinal analyses, duration of lactation was negatively associated with milk adiponectin concentrations (beta = -0.059 +/- 0.024 and -0.059 +/- 0.007, respectively; P < 0.02 for both). Maternal postpregnancy BMI was positively associated with milk adiponectin concentrations (beta = 0.08 +/- 0.02, P < 0.0001; longitudinal analysis). Mexican mothers had lower median milk adiponectin concentrations at 1 mo than did the non-Hispanic white subjects from Cincinnati (11.5 and 19.8 ng/mL; P = 0.003). CONCLUSIONS Adiponectin is present in human milk and its concentrations are associated with duration of lactation, maternal adiposity, and ethnicity. Given the importance of adiponectin in inflammation, insulin sensitivity, and fatty acid metabolism, future studies should examine milk adiponectin's role in infant metabolic development.
The distance dependence prediction of the Janzen-Connell hypothesis: a meta-analysis

The Janzen-Connell hypothesis explains the maintenance of tropical diversity through the interacting effects of parent-centered dispersal patterns and distance- and density-dependent propagule survival. These effects were thought to support regular spacing of species within tropical forest, enhancing diversity. One of the predictions of the hypothesis is that seed and seedling survival should improve with increased parental distance. Although there are many independent tests of this hypothesis for individual species, there are few synthetic studies that have brought these data together to test its validity across species. This paper reports the results of a meta-analysis of the effect of distance on enhancing propagule survival, employing an odds-ratio effect size metric. We found no general support for the distance-dependent prediction of the hypothesis, and conclude that further testing to explore this hypothesis as a diversity-maintaining mechanism is unnecessary. However, we did find that distance from parent slightly reduces survivorship in the temperate zone, as contrasted with the tropics, and we saw stronger evidence in support of the hypothesis for seedlings than for seeds. The phenomenon of enhanced propagule survival with distance from the parent may be important for the population biology of particular species, but it is not a general phenomenon across communities, life history stages or life forms.
Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction‐site associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re‐evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD‐seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans‐Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD‐seq based approaches for the resolution of complex spatial patterns, resolves a region of trans‐Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.
Spatio-temporal patterns in pelvic reduction in threespine stickleback (Gasterosteus aculeatus L.) in Lake Storvatnet

Questions: The pelvic girdle with associated spines is an integrated anti-predator defence apparatus, and is assumed to protect against piscivores in the threespine stickleback. On the other hand, it might be costly to produce the pelvic apparatus in ion-poor and mineralchallenging freshwater. Hypothesis: Stickleback with a reduced pelvic apparatus should use more shelter and be more nocturnal, avoiding predation risk. In contrast, stickleback with a well-developed pelvic apparatus should have reduced mortality during ontogeny in encounters with piscivores and thus have a longer expected lifespan. Given these two life-history strategies, we expect assortative mating as a result of divergent selection. Organism: Marine and freshwater threespine stickleback (Gasterosteus aculeatus L.). Places and times: Two representative ancestral marine populations and 36 freshwater populations in northwestern Norway (Lake Storvatnet, the main focus of the study, and three lakes downstream of it). Material was collected from 2006 to 2009. Analytical methods: We categorized nominal pelvic apparatus development (CPS morphs) in all fish, and measured metrics associated with these categories in a subsample. We also studied temporal, spatial, and habitat variation in the distribution of pelvic morphs in Lake Storvatnet. In this population, and downstream populations, we contrasted the detailed pelvic morphology with the measured genetic diversity (microsatellites), also estimating gene flow. In Lake Storvatnet, we tested for genetic divergence and signs of potential build-up of reproductive isolation via assortative mating among the observed nominal categories of pelvic reduction (CPS). Results: Pelvic reduction was seen only in Lake Storvatnet, where more than 50% of fish had a reduced pelvis. The distribution of pelvic morphs was stable over time and did not differ between habitats. The proportion of fish with pelvic reduction decreased with age. Freshwater
Light-Field Capture by Multiplexing in the Frequency Domain

In previous works light-field capture has been analyzed in spatio-angular representation. A light-field camera samples the optical signal within a single photograph by multiplexing the 4D radiance onto the physical 2D surface of the sensor. In this paper we develop a theory of multiplexing the radiance in the frequency domain by optically mixing different spatial and angular frequency components and then capturing the signal by the sensor. We derive a mathematical method for recovering the multiplexed spatial and angular information from the frequency representation. We have developed several prototypes of those frequency domain light-field cameras. They fall into two classes: (1) based on arrays of "active" optical elements, like lenses and prisms, and (2) based on "passive" optical elements, like masks, meshes or pinholes. Both types of cameras are understood and described in a single mathematical formalism in frequency domain. We show examples of novel view synthesis and refocusing based on this frequency domain multiplexing and discuss a number of advantages of the new method.
The interplay between dispersal and gene flow in anadromous Arctic char (Salvelinus alpinus): implications for potential for local adaptation

Dispersal can influence the process of local adaptation, particularly when the dispersers successfully breed in the non-natal habitat. Anadromous Arctic char (Salvelinus alpinus) display a complex migratory behaviour that makes the distinction between breeding and nonbreeding dispersal especially important. This species does not reproduce every year, but individuals must migrate to fresh water to overwinter such that a large proportion of fish running up-river are not in breeding condition and have no potential for gene flow. We used a genetic assignment approach to identify dispersers among populations of char from Baffin Island, Canada. Estimates of dispersal varied between 15.8% and 25.5% depending on the assignment method, suggesting that Arctic char disperse at a higher rate than other salmonids. Nonbreeding individuals were more likely to use non-natal habitats than breeding individuals, thus resulting in estimates of dispersal that overestimate the potential for gene flow among populations. Finally, we parameterized a population genetic model showing that gene flow is probably sufficiently low to allow for local adaptation among populations, given realistic selection coefficients. Our results underscore the importance of under- standing patterns of dispersal to appropriately evaluate their potential consequences for local adaptation and management. Resume : La dispersion a une influence importante sur l'adaptation locale, particulierement lorsque les migrants se reprodu- isent dans l'habitat non-natif. L'omble chevalier anadrome (Salvelinus alpinus) a un comportement migratoire complexe qui rend importante la distinction entre une dispersion suivie ou non d'une reproduction. Les individus de cette espece ne se reproduisent pas chaque annee, mais doivent tous migrer en eau douce pour hiverner. Une importante proportion d'individus migrants ne sont donc pas en etat de se reproduire et n'ont aucune influence sur le flux de genes. Nous avons utilise une approche d'assignation genetique pour identifier les individus disperseurs entre des populations d'omble chevalier de l'Ile de Baffin, Canada. Les estimes de dispersion obtenus varient entre 15.8 % et 25.5 % selon la methode d'assignation, suggerant que la dispersion est plus importante chez l'omble chevalier que chez d'autres salmonides. De plus, les individus nonreproducteurs etaient plus susceptibles d'utiliser un habitat non-natif que les individus reproducteurs, ce qui resulte en des estimes de dispersion qui surestiment le potentiel pour le flux de genes entre populations. Finalement, nous avons parametre un modele de genetique des populations qui montrent que le flux de genes pourrait etre suffisamment bas pour permettre l'evolution de l'adaptation locale a l'echelle de la riviere en supposant des coefficients de selection realistes. Nos resultats soulignent l'importance de comprendre les patrons de dispersion afin de proprement evaluer leurs consequences pour l'adaptation locale et la gestion.
Spectral scaling and good expansion properties in complex networks

The existence of a scaling between the principal eigenvector and the subgraph centrality of a complex network indicates that the network has “good expansion” (GE) properties. GE is the important but counterintuitive property of being both sparsely populated and highly connected. We have detected GE properties in half of the 16 real-world networks studied, which include communication, information and biological networks. Most of social networks studied do not show GE properties as a consequence of the existence of communities with low number of inter-community links. However, the majority of food webs represent ecosystems that are not composed of separate communities with low interconnections among them and possess GE properties.
Impact of body bias on soft error tolerance of bulk and Silicon on Thin BOX structure in 65-nm process

We analyze the soft error tolerance of DFF in 65-nm bulk and SOTB (Silicon on Thin BOX) process by alpha and neutron experiments and device-simulations. The experimental results reveal that by increasing the reverse body bias the soft error rate in the bulk structure is increased, while the number of soft errors in SOTB structure is decreased. The results from device-simulation show that the collected charge of bulk structure is increased, while the collected charge is decreased in SOTB as the reverse body bias increases.
Long noncoding RNA CCAT2 as a novel biomaker of metastasis and prognosis in human cancer: a meta-analysis

Colon cancer-associated transcript2 (CCAT2), a long noncoding RNA (LncRNA), has been found to function as an oncogene in various cancers. However, the clinical value of CCAT2 in cancers remains unclear. Therefore, we performed this meta-analysis to investigate the association between CCAT2 level and metastasis & prognosis in malignant tumors. The meta analysis was performed by using a systematic search in PubMed, Web of Science, and Cochrane Library from inception to NOV 17, 2016. According to the inclusion and exclusion criteria,9 studies with 1084 patients were included in the meta-analysis.The result showed that overexpression of CCAT2 is positively correlated with lymph node metastasis (Odds ratio,OR=3.57, 95 % confidence interval(CI): 1.79-7.13, p<0.001) in a random-effects model (I2=71%, p=0.008) and distant metastasis(OR=7.68, 95 % CI: 3. 29-17.96, p<0.001) in a random-effects model (I2=41.9%, p=0.16). Likewise,we also found that high CCAT2 expression could predict unfavourable overall survival with pooled hazard ratio (HR) of 2.23 (95 % CI 1.68-2.96, p<0.00001) by a random-effects model (I2=37.5%, p=0.143) and poor metastasis-free survival in cancer patients (HR= 2.08, 95%CI:1.37-3.18 p=0.001) by a fixed-effects model (I2=0.0%, p=0.807). In conclusion,CCAT2 might be served as a novel molecular marker for predicting metastasis and prognosis in various human-cancers.
TMP21 modulates cell growth in papillary thyroid cancer cells by inducing autophagy through activation of the AMPK/mTOR pathway.

OBJECTIVE To investigate the role of transmembrane protein (TMP) 21 in human thyroid cancer. METHODS The recombinant expression vector pcDNA3.1 (+)-TMP21 and specific small interfering RNAs (siRNA) against TMP21 were transfected into a papillary thyroid cancer cell line (TPC1). After transfection, the expression of TMP21 was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. Moreover, cell viability and apoptosis rate were respectively determined by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) colorimetric assay and flow cytometry (FCM). Additionally, Western blotting was performed to analyze the adenosine monophosphate (AMP)-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathways associated protein (P-AMPKα(Thr172), P-mTOR(Ser2448), light chain (LC)-II/LC3-I, and P-S6K(Thr389)) after pre-treatment with AMPK inhibitor, compound C (Com C) and siTMP21. RESULTS The TMP21 protein level and cell viability were significantly higher, but apoptotic rate was significantly lower by transfection with pcDNA3.1-TMP21 than those in control group (P < 0.05), and reverse results were obtained by transfection with siTMP21. However, qRT-PCR showed different results due to the feedback inhibition of mRNA. Besides, silencing of TMP21 significantly reduced the levels of P-mTOR(Ser2448) and P-S6K(Thr389) (P < 0.05), but significantly increased the levels of P-AMPKα(Thr172) and LC3-II/LC3-I compared with the control group (P < 0.01). Whereas, the levels of P-AMPKα(Thr172) and LC3-II/LC3-I were significantly decreased by Com C compared with the control group (P < 0.05). CONCLUSION TMP21 modulates cell growth in TPC1 cells by inducing autophagy, which may be associated with activation of AMPK/mTOR pathway.
Soybean phytochemicals inhibit the growth of transplantable human prostate carcinoma and tumor angiogenesis in mice.

The objectives of our studies are to characterize the ability of dietary soybean components to inhibit the growth of prostate cancer in mice and alter tumor biomarkers associated with angiogenesis. Soy isoflavones (genistein or daidzein) or soy phytochemical concentrate inhibit the growth of prostate cancer cells LNCaP, DU 145 and PC-3 in vitro, but only at supraphysiologic concentrations, i.e., 50% inhibitory concentration (IC(50)) > 50 micromol/L. G2-M arrest and DNA fragmentation consistent with apoptosis of prostate cancer cells are also observed at concentrations causing growth inhibition. In contrast, the in vitro proliferation of vascular endothelial cells was inhibited by soy phytochemcials at much lower concentrations. We evaluated the ability of dietary soy phytochemical concentrate and soy protein isolate to inhibit the growth of the LNCaP human prostate cancer in severe combined immune-deficient mice. Mice inoculated subcutaneously with LNCaP cells (2 x 10(6)) were randomly assigned to one of the six dietary groups based on the AIN-76A formulation for 3 wk. A 2 x 3 factorial design was employed with two protein sources (20%, casein vs. soy protein) and three levels of soy phytochemical concentrate (0, 0.2 and 1.0% of the diet). Soy components did not alter body weight gain or food intake. Compared with casein-fed controls, the tumor volumes after 3 wk were reduced by 11% (P = 0.45) by soy protein, 19% (P = 0.17) by 0.2% soy phytochemical concentrate, 28% by soy protein with 0.2% soy phytochemical concentrate (P < 0.05), 30% by 1.0% soy phytochemical concentrate (P < 0.05) and 40% by soy protein with 1.0% soy phytochemical concentrate (P < 0.005). Histologic examination of tumor tissue showed that consumption of soy products significantly reduced tumor cell proliferation, increased apoptosis and reduced microvessel density. The angiogenic protein insulin-like growth factor-I was reduced in the circulation of mice fed soy protein and phytochemical concentrate. Our data suggest that dietary soy products may inhibit experimental prostate tumor growth through a combination of direct effects on tumor cells and indirect effects on tumor neovasculature.