Semi-Supervised Contrastive Learning for Remote Sensing: Identifying Ancient Urbanization in the South-Central Andes.

Archaeology has long faced fundamental issues of sampling and scalar representation. Traditionally, the local-to-regional-scale views of settlement patterns are produced through systematic pedestrian surveys. Recently, systematic manual survey of satellite and aerial imagery has enabled continuous distributional views of archaeological phenomena at interregional scales. However, such "brute force" manual imagery survey methods are both time- and labor-intensive, as well as prone to inter-observer differences in sensitivity and specificity. The development of self-supervised learning methods (e.g., contrastive learning) offers a scalable learning scheme for locating archaeological features using unlabeled satellite and historical aerial images. However, archaeological features are generally only visible in a very small proportion relative to the landscape, while the modern contrastive-supervised learning approach typically yields an inferior performance on highly imbalanced datasets. In this work, we propose a framework to address this long-tail problem. As opposed to the existing contrastive learning approaches that typically treat the labeled and unlabeled data separately, our proposed method reforms the learning paradigm under a semi-supervised setting in order to fully utilize the precious annotated data (<7% in our setting). Specifically, the highly unbalanced nature of the data is employed as the prior knowledge in order to form pseudo negative pairs by ranking the similarities between unannotated image patches and annotated anchor images. In this study, we used 95,358 unlabeled images and 5,830 labeled images in order to solve the issues associated with detecting ancient buildings from a long-tailed satellite image dataset. From the results, our semi-supervised contrastive learning model achieved a promising testing balanced accuracy of 79.0%, which is a 3.8% improvement as compared to other state-of-the-art approaches.

Hemodynamic Response Function in Brain White Matter in a Resting State.

The hemodynamic response function (HRF) characterizes temporal variations of blood oxygenation level-dependent (BOLD) signals. Although a variety of HRF models have been proposed for gray matter responses to functional demands, few studies have investigated HRF profiles in white matter particularly under resting conditions. In the present work we quantified the nature of the HRFs that are embedded in resting state BOLD signals in white matter, and which modulate the temporal fluctuations of baseline signals. We demonstrate that resting state HRFs in white matter could be derived by referencing to intrinsic avalanches in gray matter activities, and the derived white matter HRFs had reduced peak amplitudes and delayed peak times as compared with those in gray matter. Distributions of the time delays and correlation profiles in white matter depend on gray matter activities as well as white matter tract distributions, indicating that resting state BOLD signals in white matter encode neural activities associated with those of gray matter. This is the first investigation of derivations and characterizations of resting state HRFs in white matter and their relations to gray matter activities. Findings from this work have important implications for analysis of BOLD signals in the brain.

Transient flow-driven distortion of a nematic liquid crystal in channel flow with dissipative weak planar anchoring.

Motivated by the one-drop-filling (ODF) method for the industrial manufacturing of liquid crystal displays, we analyze the pressure-driven flow of a nematic in a channel with dissipative weak planar anchoring at the boundaries of the channel. We obtain quasisteady asymptotic solutions for the director angle and the velocity in the limit of small Leslie angle, in which case the key parameters are the Ericksen number and the anchoring strength parameter. In the limit of large Ericksen number, the solution for the director angle has narrow reorientational boundary layers and a narrow reorientational internal layer separated by two outer regions in which the director is aligned at the positive Leslie angle in the lower half of the channel and the negative Leslie angle in the upper half of the channel. On the other hand, in the limit of small Ericksen number, the solution for the director angle is dominated by splay elastic effects with viscous effects appearing at first order. As the Ericksen number varies, there is a continuous transition between these asymptotic behaviors, and in fact the two asymptotic solutions capture the behavior rather well for all values of the Ericksen number. The steady-state value of the director angle at the boundaries and the timescale of the evolution toward this steady-state value in the asymptotic limits of large and small Ericksen number are determined. In particular, using estimated parameter values for the ODF method, it is found that the boundary director rotation timescale is substantially shorter than the timescale of the ODF method, suggesting that there is sufficient time for significant transient flow-driven distortion of the nematic molecules at the substrates from their required orientation to occur.

Th17 Responses to Collagen Type V, kα1-Tubulin, and Vimentin Are Present Early in Human Development and Persist Throughout Life.

T helper 17 (Th17)-dependent autoimmune responses can develop after heart or lung transplantation and are associated with fibro-obliterative forms of chronic rejection; however, the specific self-antigens involved are typically different from those associated with autoimmune disease. To investigate the basis of these responses, we investigated whether removal of regulatory T cells or blockade of function reveals a similar autoantigen bias. We found that Th17 cells specific for collagen type V (Col V), kα1-tubulin, and vimentin were present in healthy adult peripheral blood mononuclear cells, cord blood, and fetal thymus. Using synthetic peptides and recombinant fragments of the Col V triple helical region (α1[V]), we compared Th17 cells from healthy donors with Th17 cells from Col V-reactive heart and lung patients. Although the latter responded well to α1(V) fragments and peptides in an HLA-DR-restricted fashion, Th17 cells from healthy persons responded in an HLA-DR-restricted fashion to fragments but not to peptides. Col V, kα1-tubulin, and vimentin are preferred targets of a highly conserved, hitherto unknown, preexisting Th17 response that is MHC class II restricted. These data suggest that autoimmunity after heart and lung transplantation may result from dysregulation of an intrinsic mechanism controlling airway and vascular homeostasis.

Asymmetric band gap shift in electrically addressed blue phase photonic crystal fibers.

In this paper, we present electrooptic experiments on photonic crystal fibers filled with a liquid crystalline blue phase. These fibers guide light via photonic band gaps (PBGs). The blue phase is isotropic in the field-off state but becomes birefringent under an electric field. This leads to a polarization dependent shift of the PBGs. Interestingly, the effect on the PBGs is asymmetrical: while the short wavelength edges of the PBGs shift, the long wavelength edges are almost unaffected. By performing band gap and modal analyses via the finite element simulations, we find that the asymmetric shift is the result of the mixed polarization of the involved photonic bands. Finally, we use the band gap shifts to calculate effective Kerr constants of the blue phase.

Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation.

Improved diagnostic methods are needed for bronchiolitis obliterans syndrome (BOS), a serious complication after allogeneic hematopoietic cell transplantation (HCT) and lung transplantation. For protein candidate discovery, we compared plasma pools from HCT transplantation recipients with BOS at onset (n = 12), pulmonary infection (n = 16), chronic graft-versus-host disease without pulmonary involvement (n = 15) and no chronic complications after HCT (n = 15). Pools were labeled with different tags (isobaric tags for relative and absolute quantification), and two software tools identified differentially expressed proteins (≥1.5-fold change). Candidate proteins were further selected using a six-step computational biology approach. The diagnostic value of the lead candidate, matrix metalloproteinase 3 (MMP3), was evaluated by enzyme-linked immunosorbent assay in plasma of a verification cohort (n = 112) with and without BOS following HCT (n = 76) or lung transplantation (n = 36). MMP3 plasma concentrations differed significantly between patients with and without BOS (area under the receiver operating characteristic curve 0.77). Consequently, MMP3 represents a potential noninvasive blood test for diagnosis of BOS.

Protein Quantitative Trait Loci Analysis Identifies Genetic Variation in the Innate Immune Regulator TOLLIP in Post-Lung Transplant Primary Graft Dysfunction Risk.

The authors previously identified plasma plasminogen activator inhibitor-1 (PAI-1) level as a quantitative lung injury biomarker in primary graft dysfunction (PGD). They hypothesized that plasma levels of PAI-1 used as a quantitative trait could facilitate discovery of genetic loci important in PGD pathogenesis. A two-stage cohort study was performed. In stage 1, they tested associations of loci with PAI-1 plasma level using linear modeling. Genotyping was performed using the Illumina CVD Bead Chip v2. Loci meeting a p < 5 × 10(-4) cutoff were carried forward and tested in stage 2 for association with PGD. Two hundred ninety-seven enrollees were evaluated in stage 1. Six loci, associated with PAI-1, were carried forward to stage 2 and evaluated in 728 patients. rs3168046 (Toll interacting protein [TOLLIP]) was significantly associated with PGD (p = 0.006). The increased risk of PGD for carrying at least one copy of this variant was 11.7% (95% confidence interval 4.9-18.5%). The false-positive rate for individuals with this genotype who did not have PGD was 6.1%. Variants in the TOLLIP gene are associated with higher circulating PAI-1 plasma levels and validate for association with clinical PGD. A protein quantitative trait analysis for PGD risk prioritizes genetic variations in TOLLIP and supports a role for Toll-like receptors in PGD pathogenesis.

Objective Estimates Improve Risk Stratification for Primary Graft Dysfunction after Lung Transplantation.

Primary graft dysfunction (PGD) is a major cause of early mortality after lung transplant. We aimed to define objective estimates of PGD risk based on readily available clinical variables, using a prospective study of 11 centers in the Lung Transplant Outcomes Group (LTOG). Derivation included 1255 subjects from 2002 to 2010; with separate validation in 382 subjects accrued from 2011 to 2012. We used logistic regression to identify predictors of grade 3 PGD at 48/72 h, and decision curve methods to assess impact on clinical decisions. 211/1255 subjects in the derivation and 56/382 subjects in the validation developed PGD. We developed three prediction models, where low-risk recipients had a normal BMI (18.5-25 kg/m(2) ), chronic obstructive pulmonary disease/cystic fibrosis, and absent or mild pulmonary hypertension (mPAP<40 mmHg). All others were considered higher-risk. Low-risk recipients had a predicted PGD risk of 4-7%, and high-risk a predicted PGD risk of 15-18%. Adding a donor-smoking lung to a higher-risk recipient significantly increased PGD risk, although risk did not change in low-risk recipients. Validation demonstrated that probability estimates were generally accurate and that models worked best at baseline PGD incidences between 5% and 25%. We conclude that valid estimates of PGD risk can be produced using readily available clinical variables.

Resource estimation in high performance medical image computing.

Medical imaging analysis processes often involve the concatenation of many steps (e.g., multi-stage scripts) to integrate and realize advancements from image acquisition, image processing, and computational analysis. With the dramatic increase in data size for medical imaging studies (e.g., improved resolution, higher throughput acquisition, shared databases), interesting study designs are becoming intractable or impractical on individual workstations and servers. Modern pipeline environments provide control structures to distribute computational load in high performance computing (HPC) environments. However, high performance computing environments are often shared resources, and scheduling computation across these resources necessitates higher level modeling of resource utilization. Submission of 'jobs' requires an estimate of the CPU runtime and memory usage. The resource requirements for medical image processing algorithms are difficult to predict since the requirements can vary greatly between different machines, different execution instances, and different data inputs. Poor resource estimates can lead to wasted resources in high performance environments due to incomplete executions and extended queue wait times. Hence, resource estimation is becoming a major hurdle for medical image processing algorithms to efficiently leverage high performance computing environments. Herein, we present our implementation of a resource estimation system to overcome these difficulties and ultimately provide users with the ability to more efficiently utilize high performance computing resources.

Differential requirement for P2X7R function in IL-17 dependent vs. IL-17 independent cellular immune responses.

IL17-dependent autoimmunity to collagen type V (Col V) has been associated with lung transplant obliterative bronchiolitis. Unlike the T helper 1 (Th1)-dependent immune responses to Tetanus Toxoid (TT), the Th17 response to Col V in lung transplant patients and its Th1/17 variant observed in coronary artery disease patients requires IL-1ß, tumor necrosis factor α and CD14(+) cells. Given the involvement of the P2X7 receptor (P2X7R) in monocyte IL-1ß responses, we investigated its role in Th17-, Th1/17- and Th1-mediated proinflammatory responses. Transfer of antigen-pulsed peripheral blood mononucleated cells (PBMCs) from Col V-reactive patients into SCID mouse footpads along with P2X7R antagonists revealed a selective inhibition of Col V-, but not TT-specific swelling responses. P2X7R inhibitors blocked IL-1ß induction from monocytes, including both Col V-α1 peptide-induced (T-dependent), as well as native Col V-induced (T-independent) responses. Significantly higher P2X7R expression was found on CXCR3(neg) CCR4(+)/6(+) CD4(+) [Th17] versus CXCR3(+)CCR4/6(neg) CD4(+) [Th1] subsets in PBMCs, suggesting that the paradigm of selective dependence on P2X7R might extend beyond Col V autoimmunity. Indeed, P2X7R inhibitors suppressed not only anti-Col V, but also Th1/17-mediated alloimmunity, in a heart transplant patient without affecting anti-viral Epstein-Barr virus responses. These results suggest that agents targeting the P2X7R might effectively treat Th17-related transplant pathologies, while maintaining Th1-immunity to infection.

Preoperative plasma club (clara) cell secretory protein levels are associated with primary graft dysfunction after lung transplantation.

Inherent recipient factors, including pretransplant diagnosis, obesity and elevated pulmonary pressures, are established primary graft dysfunction (PGD) risks. We evaluated the relationship between preoperative lung injury biomarkers and PGD to gain further mechanistic insight in recipients. We performed a prospective cohort study of recipients in the Lung Transplant Outcomes Group enrolled between 2002 and 2010. Our primary outcome was Grade 3 PGD on Day 2 or 3. We measured preoperative plasma levels of five biomarkers (CC-16, sRAGE, ICAM-1, IL-8 and Protein C) that were previously associated with PGD when measured at the postoperative time point. We used multivariable logistic regression to adjust for potential confounders. Of 714 subjects, 130 (18%) developed PGD. Median CC-16 levels were elevated in subjects with PGD (10.1 vs. 6.0, p<0.001). CC-16 was associated with PGD in nonidiopathic pulmonary fibrosis (non-IPF) subjects (OR for highest quartile of CC-16: 2.87, 95% CI: 1.37, 6.00, p=0.005) but not in subjects with IPF (OR 1.38, 95% CI: 0.43, 4.45, p=0.59). After adjustment, preoperative CC-16 levels remained associated with PGD (OR: 3.03, 95% CI: 1.26, 7.30, p=0.013) in non-IPF subjects. Our study suggests the importance of preexisting airway epithelial injury in PGD. Markers of airway epithelial injury may be helpful in pretransplant risk stratification in specific recipients.

Chemically induced twist-bend nematic liquid crystals, liquid crystal dimers, and negative elastic constants.

Here we report the chemical induction of the twist-bend nematic phase in a nematic mixture of ether-linked liquid crystal dimers by the addition of a dimer with methylene links; all dimers have an odd number of groups in the spacer connecting the two mesogenic groups. The twist-bend phase has been identified from its optical texture and x-ray scattering pattern as well as NMR spectroscopy, which demonstrates the phase chirality. Theory predicts that the key macroscopic property required for the stability of this chiral phase formed from achiral molecules is for the bend elastic constant to tend to be negative; in addition the twist elastic constant should be smaller than half the splay elastic constant. To test these important aspects of the prediction we have measured the bend and splay elastic constants in the nematic phase preceding the twist-bend nematic using the classic Frederiks methodology and all three elastic constants employing the dynamic light scattering approach. Our results show that, unlike the splay, the bend elastic constant is small and decreases significantly as the transition to the induced twist-bend nematic phase is approached, but then exhibits unexpected behavior prior to the phase transition.

Elevated plasma long pentraxin-3 levels and primary graft dysfunction after lung transplantation for idiopathic pulmonary fibrosis.

Primary graft dysfunction (PGD) after lung transplantation may result from ischemia reperfusion injury (IRI). The innate immune response to IRI may be mediated by Toll-like receptor and IL-1-induced long pentraxin-3 (PTX3) release. We hypothesized that elevated PTX3 levels were associated with PGD. We performed a nested case control study of lung transplant recipients with idiopathic pulmonary fibrosis (IPF) or chronic obstructive pulmonary disease (COPD) from the Lung Transplant Outcomes Group cohort. PTX3 levels were measured pretransplant, and 6 and 24 h postreperfusion. Cases were subjects with grade 3 PGD within 72 h of transplantation and controls were those without grade 3 PGD. Generalized estimating equations and multivariable logistic regression were used for analysis. We selected 40 PGD cases and 79 non-PGD controls. Plasma PTX3 level was associated with PGD in IPF but not COPD recipients (p for interaction < 0.03). Among patients with IPF, PTX3 levels at 6 and 24 h were associated with PGD (OR = 1.6, p = 0.02 at 6 h; OR = 1.4, p = 0.008 at 24 h). Elevated PTX3 levels were associated with the development of PGD after lung transplantation in IPF patients. Future studies evaluating the role of innate immune activation in IPF and PGD are warranted.

Neutralizing IL-17 prevents obliterative bronchiolitis in murine orthotopic lung transplantation.

Obliterative bronchiolitis (OB) is the key impediment to the long-term survival of lung transplant recipients and the lack of a robust preclinical model precludes examining OB immunopathogenesis. In the current study, lungs from C57BL/10 H-2(b) mice that are MHC compatible, but minor histocompatability antigen incompatible, were transplanted into C57BL/6 mice. Histological features and cytokine profiles of OB were assessed. Moderate rejection (grade A3) developed by day 14, with evidence of OB at that time point. At 21 days, OB was present in 55% of grafts and moderate to severe rejection (grade A3-A4) was present in all mice. At 28 days, OB was present in 44% of mice and severe rejection (grade A4) was present in all. IL-17A, but not IL-17F, splenic mRNA transcripts and serum protein levels were increased only in mice that developed OB, whereas IL-10 transcripts and protein were increased only in non-OB mice. Neutralizing IL-17 prevented OB, down regulated acute rejection, and upregulated systemic IL-10. Collectively, these data show that transplantation of minor histoincompatible lungs from C57BL/10 mice into C57BL/6 mice results in a highly reproducible preclinical model of OB. In addition, these data indicate that neutralizing IL-17A or augmenting IL-10 could be therapeutic interventions to prevent OB.

Immunobiology of chronic lung allograft dysfunction: new insights from the bench and beyond.

The first successful human lung transplants were performed in the 1980s. Since that time lung transplantation has been a therapeutic modality for end-stage pulmonary diseases. However, chronic rejection, known as obliterative bronchiolitis (OB)/bronchiolitis obliterans syndrome (BOS), is the key reason why the 5-year survival is only 50%, which is significantly worse than most other solid organ transplants. Recent studies have provided exciting advances that are beginning to be translated into findings in humans. This review will highlight the current advances in understanding the mechanisms of OB/BOS in lung transplant recipients.

Silencing S1P1 receptors regulates collagen-V reactive lymphocyte-mediated immunobiology in the transplanted lung.

Type V collagen (col[V])-reactive lymphocytes contribute to lung transplant rejection, but the mechanisms for emigration into the graft are unknown. Sphingosine-1-phosphate-1 receptors (S1P(1R)) are believed to be required for lymphocyte emigration in other studies, but their role in col(V)-reactive lymphocyte rejection responses is not known. Utilizing small interfering RNA (siRNA) to reduce S1P(1R) expression on col(V)-reactive lymphocytes, we examined the role of S1P(1R) in the rejection response. Quantitative polymerase chain reaction (PCR) revealed strong expression of S1P(1R) messenger RNA (mRNA)on col(V)-reactive lymphocytes isolated from immunized rats. S1P(1R)-specific siRNA (S1P(1R) siRNA) reduced expression of S1P(1R) mRNA and protein, whereas scramble siRNA (SC siRNA) had no effect. Adoptive transfer of lymphocytes treated with S1P(1R) siRNA to rat Wistar Kyoto (WKY) lung isograft recipients resulted in retention of cells within the liver with fewer cells in mediastinal lymph nodes when compared to cells exposed to SC siRNA. S1P(1R)-deficient cells proliferated in response to alloantigens, but not in response to col(V), and produced less interferon (IFN)-gamma in response to col(V) compared to controls. Downregulating S1P(1R) did not affect production of interleukin (IL)-10and tumor necrosis factor (TNF)-alpha, or expression of adhesion molecules critical for migration, but prevented rejection pathology and lowered local levels of IFN-gamma post adoptive transfer. These data demonstrate novel roles of S1P(1R,) which include regulating emigration and modulating lymphocyte activation.

Audience-contingent variation in action demonstrations for humans and computers.

People may exhibit two kinds of modifications when demonstrating action for others: modifications to facilitate bottom-up, or sensory-based processing; and modifications to facilitate top-down, or knowledge-based processing. The current study examined actors' production of such modifications in action demonstrations for audiences that differed in their capacity for intentional reasoning. Actors' demonstrations of complex actions for a non-anthropomorphic computer system and for people (adult and toddler) were compared. Evidence was found for greater highlighting of top-down modifications in the demonstrations for the human audiences versus the computer audience. Conversely, participants highlighted simple perceptual modifications for the computer audience, producing more punctuated and wider ranging motions. This study suggests that people consider differences in their audiences when demonstrating action.

Lung transplant metalloproteinase levels are elevated prior to bronchiolitis obliterans syndrome.

Parenchymal disease in the allograft lung is associated with interstitial remodeling believed to be mediated by matrix metalloproteinases (MMPs). Recent studies suggest high levels of MMP-9 are associated with bronchiolitis obliterans syndrome (BOS) in lung transplant recipients. Since BOS occurs late in the posttransplant period and may be preceded by episodes of acute rejection or infection, which are associated with interstitial remodeling, we examined MMP profiles in allograft bronchoalveolar lavage (BAL) fluid in the early posttransplant period (preceding BOS). Gelatin zymography, protein array analysis and specific ELISA on BAL fluids from transplanted lungs indicated that MMP-8, MMP-9 and TIMP-1 were strongly expressed in allograft BAL fluid from stable patients, or those with infection or rejection compared to BAL fluid from normal volunteers. Elevated expression of MMP-8, MMP-9 and TIMP-1 occurred early, and was sustained for the 3.2 years covered in this study. Elevations of MMP-8, MMP-9 and TIMP-1 in the first 2 years posttransplant appear to be associated with lung transplantation itself, and not infection or rejection. These data suggest that ongoing and clinically silent MMP activity could perpetuate progressive disease in the allograft lung.

Anti-type V collagen lymphocytes that express IL-17 and IL-23 induce rejection pathology in fresh and well-healed lung transplants.

Immunity to collagen V [col(V)] contributes to lung 'rejection.' We hypothesized that ischemia reperfusion injury (IRI) associated with lung transplantation unmasks antigenic col(V) such that fresh and well-healed lung grafts have differential susceptibility to anti-col(V)-mediated injury; and expression of the autoimmune cytokines, IL-17 and IL-23, are associated with this process. Adoptive transfer of col(V)-reactive lymphocytes to WKY rats induced grade 2 rejection in fresh isografts, but induced worse pathology (grade 3) when transferred to isograft recipients 30 days post-transplantation. Immunhistochemistry detected col(V) in fresh and well-healed isografts but not native lungs. Hen egg lysozyme-reactive lymphocytes (HEL, control) did not induce lung disease in any group. Col(V), but not HEL, immunization induced transcripts for IL-17 and IL-23 (p19) in the cells utilized for adoptive transfer. Transcripts for IL-17 were upregulated in fresh, but not well-healed isografts after transfer of col(V)-reactive cells. These data show that IRI predisposes to anti-col(V)-mediated pathology; col(V)-reactive lymphocytes express IL-17 and IL-23; and anti-col(V)-mediated lung disease is associated with local expression of IL-17. Finally, because of similar histologic patterns, the pathology of clinical rejection may reflect the activity of autoimmunity to col(V) and/or alloimmunity.