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Since its first formulations almost a century ago, mathematical models for disease spreading contributed to understand, evaluate and control the epidemic processes. They promoted a dramatic change in how epidemiologists thought of the propagation of infectious diseases. In the last decade, when the traditional epidemiological models seemed to be exhausted, new types of models were developed. These new models incorporated concepts from graph theory to describe and model the underlying social structure. Many of these works merely produced a more detailed extension of the previous results, but some others triggered a completely new paradigm in the mathematical study of epidemic processes. In this review, we will introduce the basic concepts of epidemiology, epidemic modeling and networks, to finally provide a brief description of the most relevant results in the field. [ABSTRACT FROM AUTHOR]

The macrocyclic cage metal complexes –iron(II) clathrochelates possess a range of bioactive properties. These compounds are able to inhibit T-7 RNA polymerase, suppress the amyloid fibril formation, display a high toxicity in leukemia cells, bind serum albumins [1]. This provokes interest in studying their interaction with biomolecules, particularly the proteins. Aim. To characterize the interactions between clathrochelates, bearing different number of functional groups, with serum albumins (bovine/human, BSA/HSA) by physico-chemical Methods: fluorescent and circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC). Results. The protein fluorescence quenching studies evidenced to the complex formation between the functionalized clathrochelates and albumins. This binding strongly depends on the nature of the ribbed substituents in the clathrochelate framework, an extreme binding affinity is observed for the compounds bearing carboxy groups (quenching of the BSA fluorescence up to 17 times). Upon binding, clathrochelates are able to gain optical activity and induce the pronounced CD-signal in 350-600 nm region. The shape and intensities of these CD-bands are determined by the nature and number of clathrochelate’s ribbed substituents and kind of a protein. Only an alteration of isomery of carboxyphenylsulfid substituent results in the variations of their CDbands intensity upon binding to HSA up to 63 times. In the presence of BSA and HSA, hexa carboxyphenylsulfid substituted clathrochelates evoke the CD-spectra of distinct maxima positions and intensity. Fluorescent studies at different pH and displacement method show the involving of albumins main binding sites I and II in this interaction. According to the ITC data, the thermodynamic parameters of the complex formation between hexa carboxyphenylsulfid clathrochelates and BSA are determined by the isomery of ribbed substituent’s of clathrochelates. The binding constants of such complexes are moderate, Ka ranges from 5 to 28 103M-1 and the protein-ligand binding ratio is about 1:2 for meta- and ortho- isomers and 1:1 for para- isomer of compound. Conclusions. We suggest that the structure of albumin-clathrochelate complex noticeably depends on the spatial geometry of the clathrochelates ribbed substituents. This is reflected in the optical response -the isomers of functionalized clathrochelates differently affect the protein intrinsic fluorescence and the induced CD-signal character. This high structure-sensitivity gives clathrochelate the ability to distinguish the similar proteins (BSA and HSA) by acquiring different CD-bands in their presence. [ABSTRACT FROM AUTHOR]

In this work, we analyze the origin and development of the debate on megafaunal extinctions using the Controversy Space Model (CSM). The CSM is composed of a common ground of theoretical agreements and a dialectical dynamic of disputes regarding the causes of extinction, called refocalization, identifying phases of conceptual blockage and unblockage. The hypotheses are clustered in three major groups, according to causes of extinction: anthropic, biotic, and environmental. We argue that the evolution of the controversy space follows a succession of questions relevant to each period, the answers to which need to be settled to allow the debate to move forward. We postulate that nowadays this controversy space is suffering a period of conceptual blockage. This may be because authors are assembled around two major paradigms: environmental versus anthropic causes. Each of these two theoretical positions looks at a portion of reality that may be partially true, but incomplete in terms of a global theory of extinction. We propose that this conceptual blockage could be solved by developing a mathematical model in which each hypothesis plays a role in a mechanistic way. The relative importance of each hypothesis may vary depending on its respective context. It follows from this that it should not matter which cause is favored: the emphasis should be given to all causes acting together in a predictable manner. [ABSTRACT FROM AUTHOR]

We study the flow of grains under vibration passing through a small aperture in two dimensions using discrete element method simulations. Such systems are prone to clogging and strategies to ease the flow are desirable in multiple applications. We show that the addition of low-friction particles to the system can reduce clogging and lead to an enhancement of the net flux of the original species. Along with the role of the particle friction, we analyze the influence of both the size of the added particles and the mixing ratio. We consider systems with constant height of the granular column (using particle reinjection) as well as processes of fully emptying the containing hopper.

We analyze the dynamics of room evacuation for mixed populations that include both competitive and cooperative individuals through numerical simulations using the social force model. Cooperative agents represent well-trained individuals who know how to behave in order to reduce risks within high-density crowds. We consider that competitive agents can imitate cooperative behavior when they are in close proximity to cooperators. We study the effects of the imitation of cooperative behavior on the duration and safety of evacuations, analyzing evacuation time and other quantities of interest for varying parameters such as the proportions of mixing, the aspect ratio of the room, and the parameters characterizing individual behaviors. Our main findings reveal that the addition of a relatively small number of cooperative agents into a crowd can reduce evacuation time and the density near the exit door, making the evacuation faster and safer despite an increase in the total number of agents. In particular, for long spaces such as corridors, a small number of added cooperative agents can significantly facilitate the evacuation process. We compare our results with those of systems without imitation and also study the general role of cooperation, providing further analysis for homogeneous populations. Our main conclusions emphasize the potential relevance of training people how to behave in high-density crowds.

BackgroundAcute tubulointerstitial nephritis (AIN) is one of the few causes of acute kidney injury with diagnosis-specific treatment options. However, due to the need to obtain a kidney biopsy for histological confirmation, AIN diagnosis can be delayed, missed, or incorrectly assumed. Here, we identify and validate urinary CXCL9, an IFN-γ-induced chemokine involved in lymphocyte chemotaxis, as a diagnostic biomarker for AIN.MethodsIn a prospectively enrolled cohort with pathologist-adjudicated histological diagnoses, termed the discovery cohort, we tested the association of 180 immune proteins measured by an aptamer-based assay with AIN and validated the top protein, CXCL9, using sandwich immunoassay. We externally validated these findings in 2 cohorts with biopsy-confirmed diagnoses, termed the validation cohorts, and examined mRNA expression differences in kidney tissue from patients with AIN and individuals in the control group.ResultsIn aptamer-based assay, urinary CXCL9 was 7.6-fold higher in patients with AIN than in individuals in the control group (P = 1.23 × 10-5). Urinary CXCL9 measured by sandwich immunoassay was associated with AIN in the discovery cohort (n = 204; 15% AIN) independently of currently available clinical tests for AIN (adjusted odds ratio for highest versus lowest quartile: 6.0 [1.8-20]). Similar findings were noted in external validation cohorts, where CXCL9 had an AUC of 0.94 (0.86-1.00) for AIN diagnosis. CXCL9 mRNA expression was 3.9-fold higher in kidney tissue from patients with AIN (n = 19) compared with individuals in the control group (n = 52; P = 5.8 × 10-6).ConclusionWe identified CXCL9 as a diagnostic biomarker for AIN using aptamer-based urine proteomics, confirmed this association using sandwich immunoassays in discovery and external validation cohorts, and observed higher expression of this protein in kidney biopsies from patients with AIN.FundingThis study was supported by National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) awards K23DK117065 (DGM), K08DK113281 (KM), R01DK128087 (DGM), R01DK126815 (DGM and LGC), R01DK126477 (KNC), UH3DK114866 (CRP, DGM, and FPW), R01DK130839 (MES), and P30DK079310 (the Yale O'Brien Center). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Kidney pathology education is a critical component in training of nephrology fellows, as well as for continuing medical education for practicing nephrologists. Kidney pathology images are included on nephrology fellow board exams, and clinicopathologic correlation of kidney biopsy findings is critical in everyday clinical practice. Nephropathology training is a requirement by the American College of Graduate Medical Education within nephrology fellowship curricula. However, greater than one-third of fellowship program directors believe that nephropathology training for their fellows is not sufficient. During the Coronavirus Disease-19 pandemic, the use of digital learning has become commonplace with virtual conferences (local, national, and international) and online meetings becoming the norm for education. Nephrology has become a leader in free open-access online medical education, both prior to and, to even a greater extent, during the pandemic. Here, we review available resources to nephrology fellows and other learners to supplement nephropathology training, which includes medical blogs, journal clubs, interactive quizzes and games, online conferences, podcasts, and mentorship opportunities. These resources are archived and provide durable content to learners of all stages of training, even beyond the pandemic., (Copyright © 2022 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.)

Background: Patients with acute interstitial nephritis (AIN) can present without typical clinical features, leading to a delay in diagnosis and treatment. We therefore developed and validated a diagnostic model to identify patients at risk of AIN using variables from the electronic health record., Methods: In patients who underwent a kidney biopsy at Yale University between 2013 and 2018, we tested the association of >150 variables with AIN, including demographics, comorbidities, vital signs and laboratory tests (training set 70%). We used least absolute shrinkage and selection operator methodology to select prebiopsy features associated with AIN. We performed area under the receiver operating characteristics curve (AUC) analysis with internal (held-out test set 30%) and external validation (Biopsy Biobank Cohort of Indiana). We tested the change in model performance after the addition of urine biomarkers in the Yale AIN study., Results: We included 393 patients (AIN 22%) in the training set, 158 patients (AIN 27%) in the test set, 1118 patients (AIN 11%) in the validation set and 265 patients (AIN 11%) in the Yale AIN study. Variables in the selected model included serum creatinine {adjusted odds ratio [aOR] 2.31 [95% confidence interval (CI) 1.42-3.76]}, blood urea nitrogen:creatinine ratio [aOR 0.40 (95% CI 0.20-0.78)] and urine dipstick specific gravity [aOR 0.95 (95% CI 0.91-0.99)] and protein [aOR 0.39 (95% CI 0.23-0.68)]. This model showed an AUC of 0.73 (95% CI 0.64-0.81) in the test set, which was similar to the AUC in the external validation cohort [0.74 (95% CI 0.69-0.79)]. The AUC improved to 0.84 (95% CI 0.76-0.91) upon the addition of urine interleukin-9 and tumor necrosis factor-α., Conclusions: We developed and validated a statistical model that showed a modest AUC for AIN diagnosis, which improved upon the addition of urine biomarkers. Future studies could evaluate this model and biomarkers to identify unrecognized cases of AIN., (© The Author(s) 2021. Published by Oxford University Press on behalf of the ERA.)

Background and Objectives: Uromodulin, produced exclusively in the kidney's thick ascending limb, is a biomarker of kidney tubular health. However, the relationship between urine uromodulin and histologic changes in the kidney tubulointerstitium has not been characterized. In this study, we test the association of urine uromodulin with kidney histologic findings in humans and mice., Design, Setting, Participants, & Measurements: We investigated the independent association of urine uromodulin measured at the time of kidney biopsy with histologic features in 364 participants at two academic medical centers from 2015 to 2018 using multivariable linear regression models. This relationship was further examined by comparison of uromodulin staining in murine models of kidney fibrosis and repair., Results: We found urine uromodulin to be correlated with serum creatinine (rho=-0.43; P <0.001), bicarbonate (0.20; P <0.001), and hemoglobin (0.11; P =0.03) at the time of biopsy but not with urine albumin (-0.07; P =0.34). Multivariable models controlling for prebiopsy GFR, serum creatinine at biopsy, and urine albumin showed higher uromodulin to be associated with lower severity of interstitial fibrosis/tubular atrophy and glomerulosclerosis (interstitial fibrosis/tubular atrophy: -3.5% [95% confidence intervals, -5.7% to -1.2%] and glomerulosclerosis: -3.3% [95% confidence intervals, -5.9% to -0.6%] per two-fold difference in uromodulin). However, when both interstitial fibrosis/tubular atrophy and glomerulosclerosis were included in multivariable analysis, only interstitial fibrosis/tubular atrophy was independently associated with uromodulin (interstitial fibrosis/tubular atrophy: -2.5% [95% confidence intervals, -4.6% to -0.4%] and glomerulosclerosis: -0.9% [95% confidence intervals, -3.4% to 1.5%] per two-fold difference in uromodulin). In mouse kidneys, uromodulin staining was found to be lower in the fibrotic model than in normal or repaired models., Conclusions: Higher urine uromodulin is independently associated with lower tubulointerstitial fibrosis in both human kidney biopsies and a mouse model of fibrosis., Podcast: This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022&#95;08&#95;10&#95;CJN04360422.mp3., (Copyright © 2022 by the American Society of Nephrology.)

Background: We previously demonstrated that urine interleukin (IL)-9 and tumor necrosis factor (TNF)-α can distinguish acute interstitial nephritis (AIN) from other causes of acute kidney injury. Here we evaluated the role of these biomarkers to prognosticate kidney function in patients with AIN., Methods: In a cohort of participants with biopsy-proven, adjudicated AIN, we tested the association of histological features and urine biomarkers (IL-9 and TNF-α) with estimated glomerular filtration rate measured 6 months after diagnosis (6 m-eGFR) controlling for eGFR before AIN and albuminuria. We also evaluated subgroups in whom corticosteroid use was associated with 6 m-eGFR., Results: In the 51 (93%) of the 55 participants with complete data, median (interquartile range) eGFR before and 6 m after AIN were 41 (27-69) and 28 (13-47) mL/min/1.73 m2, respectively. Patients with higher severity of interstitial fibrosis had lower 6 m-eGFR, whereas those with higher tubulointerstitial infiltrate had higher 6 m-eGFR. IL-9 levels were associated with lower 6 m-eGFR only in the subset of patients who did not receive corticosteroids [6m-eGFR per doubling of IL-9, -6.0 (-9.4 to -2.6) mL/min/1.73 m2]. Corticosteroid use was associated with higher 6 m-eGFR [20.9 (0.2, 41.6) mL/min/1.73 m2] only in those with urine IL-9 above the median (>0.66 ng/g) but not in others., Conclusions: Urine IL-9 was associated with lower 6 m-eGFR only in participants not treated with corticosteroids. Corticosteroid use was associated with higher 6 m-eGFR in those with high urine IL-9. These findings provide a framework for IL-9-guided clinical trials to test efficacy of immunosuppressive therapy in patients with AIN., (© The Author(s) 2020. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.)

Membranous lupus nephritis is a frequent cause of nephrotic syndrome in patients with systemic lupus erythematosus. It has been shown in phospholipase A2 receptor positive membranous nephropathy that known antibodies can be detected within sera, determination of the target autoantigen can have diagnostic significance, inform prognosis, and enable non-invasive monitoring of disease activity. Here we utilized mass spectrometry for antigen discovery in laser captured microdissected glomeruli from formalin-fixed paraffin embedded tissue and tissue protein G immunoprecipitation studies to interrogate immune complexes from frozen kidney biopsy tissue. We identified neural cell adhesion molecule 1 (NCAM1) to be a target antigen in some cases of membranous lupus nephritis and within rare cases of primary membranous nephropathy. The prevalence of NCAM1 association was 6.6% of cases of membranous lupus nephritis and in 2.0% of primary membranous nephropathy cases. NCAM1 was found to colocalize with IgG within glomerular immune deposits by confocal microscopy. Additionally, serum from patients with NCAM1-associated membranous nephropathy showed reactivity to NCAM1 recombinant protein on Western blotting and by indirect immunofluorescence assay, demonstrating the presence of circulating antibodies. Thus, we propose that NCAM1 is a target autoantigen in a subset of patients with membranous lupus nephritis. Future studies are needed to determine whether anti-NCAM1 antibody levels correlate with disease activity or response to therapy., (Copyright © 2020 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.)

Competing Interests: The authors declare no conflict of interest.

Patients with membranous nephropathy have an increased risk of malignancy compared to the general population, but the target antigen for malignancy-associated membranous nephropathy is unknown. To explore this, we utilized mass spectrometry for antigen discovery in malignancy-associated membranous nephropathy examining immune complexes eluted from frozen kidney biopsy tissue using protein G bead immunoglobulin capture. Antigen discovery was performed comparing cases of membranous nephropathy of unknown and known type. Mass spectrophotometric analysis revealed that nerve epidermal growth factor-like 1 (NELL1) immune complexes were uniquely present within the biopsy tissue in membranous nephropathy. Additional NELL1-positive cases were subsequently identified by immunofluorescence. In a consecutive series, 3.8% of PLA2R- and THSD7A-negative cases were NELL1-positive. These NELL1-positive cases had segmental to incomplete IgG capillary loop staining (93.4%) and dominant or co-dominant IgG1-subclass staining (95.5%). The mean age of patients with NELL1-positive membranous nephropathy was 66.8 years, with a slight male predominance (58.2%) and 33% had concurrent malignancy. Compared with PLA2R- and THSD7A-positive cases of membranous nephropathy, there was a greater proportion of cases with malignancies in the NELL1-associated group. Thus, NELL1-associated membranous nephropathy has a unique histopathology characterized by incomplete capillary loop staining, IgG1-predominance, and is more often associated with malignancy than other known types of membranous nephropathy., (Copyright © 2020 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.)

We analyze the flow and clogging of circular grains passing through a small aperture under vibration in two dimensions. Via discrete element method simulations, we show that when grains smaller than the original ones are introduced in the system as an additive, the net flow of the original species can be significantly increased. Moreover, there is an optimal radius of the additive particles that maximizes the effect. This finding may constitute the basis for technological applications not only concerning the flow of granular materials but also regarding active matter, including pedestrian evacuation.

Coronavirus Disease-19 (COVID-19), caused by the coronavirus SARS-CoV-2, was initially recognized in Wuhan, China and subsequently spread to all continents. The disease primarily affects the lower respiratory system, but may involve other organs and systems. Histopathologic evaluation of tissue from affected patients is crucial for diagnostic purposes, but also for advancing our understanding of the disease. For that reason, we developed immunohistochemical (IHC) and in situ hybridization (ISH) assays for detection of the. virus. A total of eight autopsy lungs, one placenta, and ten kidney biopsies from COVID-19 patients were stained with a panel of commercially available antibodies for IHC and commercially available RNA probes for ISH. Similarly, autopsy lungs, placentas and renal biopsies from non-COVID-19 patients were stained with the same antibodies and probes. All eight lungs and the placenta from COVID-19 patients stained positive by IHC and ISH, while the kidney biopsies stained negative by both methodologies. As expected, all specimens from non-COVID-19 patients were IHC and ISH negative. These two assays represent a sensitive and specific method for detecting the virus in tissue samples. We provide the protocols and the list of commercially available antibodies and probes for these assays, so they can be readily implemented in pathology laboratories and medical examiner offices for diagnostic and research purposes.

External driving of the Fermion reservoirs interacting with a nanoscale charge-conductor is shown to enhance its mechanical stability during resonant tunneling. This counterintuitive cooling effect is predicted despite the net energy flow into the device. Field-induced plasmon oscillations stir the energy distribution of charge carriers near the reservoir's chemical potentials into a nonequilibrium state with favored transport of low-energy electrons. Consequently, excess heating of mechanical degrees of freedom in the conductor is suppressed. We demonstrate and analyze this effect for a generic model of mechanical instability in nanoelectronic devices, covering a broad range of parameters. Plasmon-induced stabilization is suggested as a feasible strategy to confront a major problem of current-induced heating and breakdown of nanoscale systems operating far from equilibrium.

Cage metal complexes iron(ii) clathrochelates, which are inherently CD silent, were discovered to demonstrate intensive output in induced circular dichroism (ICD) spectra upon their assembly to albumins. With the aim to design clathrochelates as protein-sensitive CD reporters, the approach for the functionalization of one chelate α-dioximate fragment of the clathrochelate framework with two non-equivalent substituents was developed, and constitutional isomers of clathrochelate with two non-equivalent carboxyphenylsulfide groups were synthesized. The interaction of designed iron(ii) clathrochelates and their symmetric homologues with globular proteins (serum albumins, lysozyme, β-lactoglobulin (BLG), trypsin, insulin) was studied by protein fluorescence quenching and CD techniques. A highly-intensive ICD output of the clathrochelates was observed upon their association with albumins and BLG. It was shown that in the presence of BLG, different clathrochelate isomers gave spectra of inverted signs, indicating the stabilization of opposite configurations ( Λ or Δ ) of the clathrochelate framework in the assembly with this protein. So, we suggest that the isomerism of the terminal carboxy group determined preferable configurations of the clathrochelate framework for the fixation in the protein binding site. MALDI TOF results show the formation of BLG-clathrochelate complex with ratio 1 : 1. Based on the docking simulations, the binding of the clathrochelate molecule (all isomers) to the main BLG binding site (calyx) in its open conformation is suggested. The above results point that the variation of the ribbed substituents at the clathrochelate framework is an effective tool to achieve the specificity of clathrochelate ICD reporting properties to the target protein., Competing Interests: The authors declare no conflict of interests., (This journal is © The Royal Society of Chemistry.)

BACKGROUNDClinical diagnosis of acute interstitial nephritis (AIN) is challenging because of lack of a diagnostic biomarker and requires a kidney biopsy. We hypothesized that AIN is mediated by specific T cell subsets such that specific T cell cytokine levels could serve as biomarkers to distinguish AIN from other causes of acute kidney disease (AKD).METHODSWe enrolled consecutive sampling participants who underwent a kidney biopsy for AKD evaluation at 2 centers between 2015 and 2018. Three pathologists independently established AIN diagnosis through review of kidney biopsies. Through univariable and multivariable analysis of 12 selected urine and plasma cytokines, we identified 2 that were diagnostic of AIN.RESULTSOf the 218 participants, 32 (15%) were diagnosed with AIN by all 3 pathologists. Participants with AIN had consistently higher levels of urine TNF-α and IL-9 than those with other diagnoses, including acute tubular injury, glomerular diseases, and diabetic kidney disease, and those without any kidney disease. As compared with participants in the lowest quartile, we noted higher odds of AIN in participants in the highest quartiles of TNF-α levels (adjusted odds ratio, 10.9 [1.8, 65.9]) and IL-9 levels (7.5 [1.2, 45.7]) when controlling for blood eosinophils, leukocyturia, and proteinuria. Addition of biomarkers improved area under receiver operating characteristic curve over clinicians' prebiopsy diagnosis (0.84 [0.78, 0.91]) vs. 0.62 [(0.53, 0.71]) and a model of current tests (0.84 [0.76, 0.91] vs. 0.69 [0.58, 0.80]).CONCLUSIONSInclusion of urinary TNF-α and IL-9 improves discrimination over clinicians' prebiopsy diagnosis and currently available tests for AIN diagnosis.FUNDINGSupported by NIH awards K23DK117065, T32DK007276, K24DK090203, K23DK097201, R01DK113191, UG3-DK114866, P30DK079310; the Robert E. Leet and Clara Guthrie Patterson Trust; and American Heart Association award 18CDA34060118.

An ability of inherently achiral macrobicyclic metal complexes iron(ii) clathrochelates to acquire an induced CD (ICD) output in the visible spectral range upon interaction with bovine serum albumin (BSA) was recently discovered. In the present work, the CD-reporting properties of iron(ii) clathrochelates to proteins and the thermodynamic parameters of their binding to albumins are evaluated. It is shown that iron(ii) clathrochelates functionalized by six ribbed carboxyphenylsulfide groups are able to discriminate between serum albumins of relative structure (here human and bovine albumins) by giving distinct ICD spectra. Besides, by the variation of the shape and intensity of CD bands, these cage metal complexes reflect the pH-triggered alterations of the tertiary structure of albumins. The constitutional isomerism (ortho-, meta- or para-isomers) of terminal carboxyphenylsulfide groups of iron(ii) clathrochelates strongly affects both the character of their ICD output upon binding with proteins and the parameters of the formed guest-host associates. Using isothermal titration calorimetry, it was determined that cage metal complexes bearing meta- and ortho-isomers of carboxyphenylsulfide groups possess higher association constants (Ka ∼ 2 × 104 M-1) and clathrochelate-to-BSA binding ratios (n = 2) than the para-isomer (Ka ∼ 5 × 103 M-1, n = 1). The iron(ii) clathrochelates are suggested to be potential molecular three-dimensional scaffolds for the design of CD-sensitive reporters able to recognize specific elements of protein surfaces.

The increasing number of mass events involving large crowds calls for a better understanding of the dynamics of dense crowds. Inquiring into the possibility of a mechanical description of these dynamics, we experimentally study the crossing of dense static crowds by a cylindrical intruder, a mechanical test which is classical for granular matter. The analysis of our experiments reveals robust features in the crowds' response, comprising both similarities and discrepancies with the response of granular media. Common features include the presence of a depleted region behind the intruder and the short-range character of the perturbation. On the other hand, unlike grains, pedestrians anticipate the intruder's passage by moving much before contact and their displacements are mostly lateral, hence not aligned with the forces exerted by the intruder. Similar conclusions are reached when the intruder is not a cylinder, but a single crossing pedestrian. Thus, our work shows that pedestrian interactions even at high densities (3 to 6 ped/m 2 ) do not reduce to mechanical ones. More generally, the avoidance strategies evidenced by our findings question the incautious use of force models for dense crowds.

A series of monomethine, trimethine- and styrylcyanine dyes based on a [1,10]phenanthroline moiety was synthesized, characterized and investigated as potential fluorescent probes for nucleic acids in cell free settings and in cells. The dyes were found to be weakly fluorescent in the unbound state, whereas upon the binding to dsDNA or RNA their emission intensity raised up to 50 times (for monomethine benzothiazole derivative FT1 complexed with RNA). The strongest fluorescence intensity in assemblies with dsDNA and RNA was observed for the trimethine benzothiazole derivative FT4. The quantum yield of FT4 fluorescence in its complex with dsDNA was found to be 1.5% and the binding constant (K b ) was estimated to be 7.9 × 10 4 M -1 that is a typical value for intercalating molecules. The FT4 dye was found to be cell membrane permeable. It stains RNA rich components-the nucleoli and most probably the cytoplasmic RNA. FT4 bound to RNAs delivers a very strong fluorescence signal, which makes this easily accessible dye a potentially useful alternative to known RNA stains, e.g. expensive SYTO ® 83. The advantage of FT4 is its easy synthetic access including no chromatographic purification steps, which will be reflected in its substantially lower price.

Background and Objectives: Prior studies have shown that the APOL1 risk alleles are associated with a greater risk of HIV-associated nephropathy and FSGS among blacks who are HIV positive. We sought to determine whether the APOL1 high-risk genotype incrementally improved the prediction of these underlying lesions beyond conventional clinical factors., Design, Setting, Participants, & Measurements: In a cross-sectional study, we analyzed data from 203 blacks who are HIV positive, underwent kidney biopsies between 1996 and 2011, and were genotyped for the APOL1 G1 and G2 alleles. Predictive logistic regression models with conventional clinical factors were compared with those that also included APOL1 genotype using receiver-operating curves and bootstrapping analyses with crossvalidation., Results: The addition of APOL1 genotype to HIV-related risk factors for kidney disease in a predictive model improved the prediction of non-HIV-associated nephropathy FSGS, specifically, increasing the c statistic from 0.65 to 0.74 (P=0.04). Although two risk alleles were significantly associated with higher odds of HIV-associated nephropathy, APOL1 genotype did not add incrementally to the prediction of this specific histopathology., Conclusions: APOL1 genotype may provide additional diagnostic information to traditional clinical variables in predicting underlying FSGS spectrum lesions in blacks who are HIV positive. In contrast, although APOL1 risk genotype predicts HIV-associated nephropathy, it lacked a high c statistic sufficient for discrimination to eliminate the role of kidney biopsy in the clinical care of blacks who are HIV positive with nephrotic proteinuria or unexplained kidney disease., (Copyright © 2016 by the American Society of Nephrology.)

Isolated endarteritis of kidney transplants is increasingly recognized. Notably, microarray studies revealed absence of immunologic signatures of rejection in most isolated endarteritis biopsy samples. We investigated if isolated endarteritis responds to rejection treatment and affects kidney transplant survival. We retrospectively enrolled recipients of kidney transplant who underwent biopsies between 1999 and 2011 at seven American and Canadian centers. Exclusion criteria were recipients were blood group-incompatible or crossmatch-positive or had C4d-positive biopsy samples. After biopsy confirmation, patients were divided into three groups: isolated endarteritis (n=103), positive controls (type I acute T cell-mediated rejection with endarteritis; n=101), and negative controls (no diagnostic rejection; n=103). Primary end points were improved kidney function after rejection treatment and transplant failure. Mean decrease in serum creatinine from biopsy to 1 month after rejection treatment was 132.6 µmol/L (95% confidence interval [95% CI], 78.7 to 186.5) in patients with isolated endarteritis, 96.4 µmol/L (95% CI, 48.6 to 143.2) in positive controls (P=0.32), and 18.6 µmol/L (95% CI, 1.8 to 35.4) in untreated negative controls (P<0.001). Functional improvement after rejection treatment occurred in 80% of patients with isolated endarteritis and 81% of positive controls (P=0.72). Over the median 3.2-year follow-up period, kidney transplant survival rates were 79% in patients with isolated endarteritis, 79% in positive controls, and 91% in negative controls (P=0.01). In multivariate analysis, isolated endarteritis was associated with an adjusted 3.51-fold (95% CI, 1.16 to 10.67; P=0.03) risk for transplant failure. These data indicate that isolated endarteritis is an independent risk factor for kidney transplant failure., (Copyright © 2015 by the American Society of Nephrology.)

Distinguishing malignant mesothelioma (MM) from reactive mesothelial hyperplasia (RM) may be difficult in effusions. This study tested the hypothesis that immunocytochemistry (IC) in effusion cell blocks (CB) can distinguish MM from RM and that the results may be applied to individual specimens. External validation of a risk score (RS) model associating sensitivity and specificity was applied to an external set of MM and RM specimens from a separate institution. Forty three effusion cytology CBs of 25 confirmed malignant mesotheliomas were compared to CBs of 23 benign mesothelial effusions without inflammation and 13 reactive mesothelial proliferations associated with inflammation. Glut-1, EMA, and Desmin expression were evaluated by immunocytochemistry on CBs. Each antibody was compared using ROC values, where the area under the curve (AUC) was 0.90, 0.82, and 0.84 for Glut-1, EMA, and Desmin, respectively. Logistic regression (LR) analysis was applied to a combination of Glut-1 and EMA. A combined ROC curve was modeled for Glut-1 and EMA (AUC = 0.93). A RS = 2 × (Glut-1%) + 1 × (EMA%) was created from this ROC curve. When applied to an external set of MM and RM, the RS resulted in an ROC with AUC = 0.91. In conclusion, a RS derived from a LR of Glut-1 and EMA IC greatly improves the distinction between MM from RM cells in individual effusions. The study illustrates principles of evidence-based pathology concerning internal and external test performance in the differential diagnosis of MM versus RM., (Copyright © 2011 Wiley Periodicals, Inc.)

Recently, an association was found between nondiabetic kidney disease in African Americans and two independent sequence variants in the APOL1 gene, encoding apolipoprotein L1. In this study we determined the frequency of APOL1 risk variants in patients with biopsy-proven HIV-associated nephropathy (HIVAN) and distinctive pathological characteristics potentially driven by those risk variants. Among 76 patients with HIVAN, 60 were successfully genotyped for APOL1 G1 and G2 polymorphisms. In this cohort, 37 had two risk alleles, 18 were heterozygous, and 5 had neither risk variant. There were no differences in the pathological findings of HIVAN and the number of APOL1 risk alleles. Further, the progression to end-stage kidney disease or death did not differ by the number of risk alleles. Median renal survival was 9.3 months in patients with zero or one risk allele compared to 11.7 months in patients with two APOL1 risk alleles. Thus, our study suggests that although the majority of African-American patients with HIVAN have two APOL1 risk alleles other as yet unknown factors in the host, including genetic risk variants and environmental or viral factors, may influence the development of this disorder in those with zero or one APOL1 risk allele.

Fibrillary glomerulonephritis (GN) is an uncommon cause of rapidly progressive kidney failure. We report a case of rapidly progressive kidney failure with kidney biopsy showing crescentic GN on light microscopy and immunofluorescence showing linear/globular glomerular basement membrane (GBM) staining for immunoglobulin G and C3, consistent with anti-GBM disease. However, electron microscopy showed fibrillary deposits in the GBM, suggesting a diagnosis of fibrillary GN. As exemplified by this case, it is important to consider fibrillary GN in the differential diagnosis of crescentic GN with linear immunoglobulin G deposits within the GBM. Electron microscopy is crucial to make this diagnosis., (Copyright © 2012 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.)

Objective: Hematuria is considered a sign of active renal disease in patients with small-vessel vasculitis. In patients who are in apparent clinical remission, presence of persistent or new-onset microscopic hematuria may reflect active vasculitis, damage, or other glomerular pathology., Methods: We identified 74 patients from the Johns Hopkins Renal Pathology database between 1995 and 2009 with the diagnosis of pauciimmune glomerulonephritis (GN). Among them we identified 9 who were in clinical remission and underwent a renal biopsy for evaluation of persistent or new-onset hematuria., Results: Nine patients with small-vessel vasculitis, 8 antineutrophil cytoplasmic antibody (ANCA)-positive and 1 ANCA-negative, underwent a renal biopsy at variable time periods after remission of vasculitis (6 to 164 months) for persistent microscopic hematuria (n = 6) or new-onset microscopic hematuria (n = 3). All patients were in apparent clinical remission at the time of renal biopsy. Of the 3 patients presenting with new-onset hematuria, 2 had crescentic IgA nephropathy and 1 had healed crescentic pauciimmune GN. Of the 6 patients with persistent hematuria, 2 had arteriosclerosis, 2 had focal segmental glomerulosclerosis, and 2 had global and segmental glomerulosclerosis and healed crescentic GN, and none had active vasculitis., Conclusion: Microscopic hematuria in patients with renal vasculitis otherwise in remission could represent chronic glomerular injury from prior episode of vasculitis or may represent new glomerular pathology. Renal biopsy should be considered in these patients to guide therapy.