Miracle-dz/UniFAR-FTUs huggingface dataset:
Herbivores as drivers of negative density dependence in tropical forest saplings

Herbivores shape tropical forests In tropical forests, high local tree diversity is driven by negative density dependence, a process whereby plant performance is inhibited by closely related neighbors. Negative density dependence could be caused by competition for resources among neighbors or result from shared herbivores and pathogens. Using data from forest plots in Panama, Forrister et al. compared the contributions of these mechanisms. They found no effect of competition, but strong effects of plant chemistry and shared herbivores on coexisting Inga tree species. Science, this issue p. 1213 Damage to saplings by herbivores rather than resource competition maintains local tree diversity in tropical rainforests. Ecological theory predicts that the high local diversity observed in tropical forests is maintained by negative density–dependent interactions within and between closely related plant species. By using long-term data on tree growth and survival for coexisting Inga (Fabaceae, Mimosoideae) congeners, we tested two mechanisms thought to underlie negative density dependence (NDD): competition for resources and attack by herbivores. We quantified the similarity of neighbors in terms of key ecological traits that mediate these interactions, as well as the similarity of herbivore communities. We show that phytochemical similarity and shared herbivore communities are associated with decreased growth and survival at the sapling stage, a key bottleneck in the life cycle of tropical trees. None of the traits associated with resource acquisition affect plant performance, indicating that competition between neighbors may not shape local tree diversity. These results suggest that herbivore pressure is the primary mechanism driving NDD at the sapling stage.
Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy

Significance Cells form structures and perform functions through intricate 3D tissue organizations. However, due to tissue scattering, coherent Raman microscopy—a powerful method complementary to fluorescence imaging—suffers from limited imaging depth in tissues. Here, we develop a volumetric chemical imaging method with greater than 10-fold depth increase. We formulate a Raman-tailored tissue-clearing recipe and combine it with advanced Raman microscopies. Equipped with the toolbox of volumetric chemical imaging and analyses, we elucidate complex 3D structures, chemical compositions, and metabolic dynamics in diverse tissues including lipid synthesis throughout tumor spheroids, 3D networks of axons, vasculatures, and cell bodies in brain regions, as well as heterogeneous tumor structures and tumor metabolism. Three-dimensional visualization of tissue structures using optical microscopy facilitates the understanding of biological functions. However, optical microscopy is limited in tissue penetration due to severe light scattering. Recently, a series of tissue-clearing techniques have emerged to allow significant depth-extension for fluorescence imaging. Inspired by these advances, we develop a volumetric chemical imaging technique that couples Raman-tailored tissue-clearing with stimulated Raman scattering (SRS) microscopy. Compared with the standard SRS, the clearing-enhanced SRS achieves greater than 10-times depth increase. Based on the extracted spatial distribution of proteins and lipids, our method reveals intricate 3D organizations of tumor spheroids, mouse brain tissues, and tumor xenografts. We further develop volumetric phasor analysis of multispectral SRS images for chemically specific clustering and segmentation in 3D. Moreover, going beyond the conventional label-free paradigm, we demonstrate metabolic volumetric chemical imaging, which allows us to simultaneously map out metabolic activities of protein and lipid synthesis in glioblastoma. Together, these results support volumetric chemical imaging as a valuable tool for elucidating comprehensive 3D structures, compositions, and functions in diverse biological contexts, complementing the prevailing volumetric fluorescence microscopy.
Recent Advances in Surface Plasmon Resonance Imaging Sensors

The surface plasmon resonance (SPR) sensor is an important tool widely used for studying binding kinetics between biomolecular species. The SPR approach offers unique advantages in light of its real-time and label-free sensing capabilities. Until now, nearly all established SPR instrumentation schemes are based on single- or several-channel configurations. With the emergence of drug screening and investigation of biomolecular interactions on a massive scale these days for finding more effective treatments of diseases, there is a growing demand for the development of high-throughput 2-D SPR sensor arrays based on imaging. The so-called SPR imaging (SPRi) approach has been explored intensively in recent years. This review aims to provide an up-to-date and concise summary of recent advances in SPRi. The specific focuses are on practical instrumentation designs and their respective biosensing applications in relation to molecular sensing, healthcare testing, and environmental screening.
Exposure to Mixtures of Pollutants in Mexican Children from Marginalized Urban Areas

Background: Exposure to contaminant mixtures in developing countries is an important public health issue. Children are identified as the most susceptible group to adverse health effects due to the exposure. Objective: The aim of this study was to conduct a screening for mixture pollutants in Mexican children in urban marginalized communities. Methods: We analyzed children (aged 6–12 years old) who resided in four urban marginalized communities in San Luis Potosi, Mexico: i) Bellas Lomas (BEL), a site with vehicular traffic; ii) Tercera Chica (TC), a site with brick kilns; Iii) Rincon de San Jose (SJR), a site with a hazardous waste landfill; and (iv) Morales (MOR) a metallurgical zone with copper-arsenic and electrolytic zinc smelters. Polycyclic Aromatic Hydrocarbons (1-hydroxypyrene (1-OHP)), benzene (trans, trans-muconic acid (t,t-MA), manganese, arsenic and fluoride were quantified in urine and lead in blood samples. Findings: Our results indicate that median exposures to manganese were 4.4, 5.2, 5.8 and 6.3 µg/L for BEL, TC, SJR and MOR, respectively. For BEL, fluoride was present at a higher concentration with 2.3 mg/L followed by MOR, TC and SJR with 1.7, 1.5 and 1.2 mg/L respectively. The highest concentrations of arsenic that were found were 11 µg/L in MOR and lead concentration was reported between 4.2 and 6.8 µg/dL, in BEL, TC and MOR. 1-OHP and t,t-MA were higher in TC (0.23 µmol/mol creatinine (cr), 429.7 µg/g cr, respectively) followed by SJR (0.09 µmol/mol cr, 427.4 µg/g cr), MOR (0.03 µmol/mol cr, 258.6 µg/g cr) and BEL (0.06 µmol/mol cr, 220.6 µg/g cr). Conclusion: Considering the large number of people, especially children, exposed to multiple pollutants, it is important to design effective intervention programs that reduce exposure and the resultant risk in the numerous urban marginalized communities in Mexico.
Reaching marginalized young women for HIV prevention in Botswana: a pilot social network analysis

Almost one-fifth of Botswana’s population is infected with HIV. The Inter-Ministerial National Structural Intervention Trial is a trial to test the impact on HIV rates of a structural intervention that refocuses government structural support programs in favor of young women. Ensuring that the intervention reaches all vulnerable young women in any given community is a challenge. Door-to-door recruitment was inefficient in previous work, so we explored innovative ways to reach this population. We sought to understand the support networks of marginalized young women, and to test the possibility of using social networks to support universal recruitment in this population. Ego-centric and sociometric analyses were used to describe the support networks of marginalized young women. Marginalized young women go to other women and relatives for support, and they communicate face to face rather than using social media. Network maps show how young women were connected to each other. Lessons from the pilot include a better understanding of how to use social networks as a recruitment method, such as the time required and the types of community members that can help. Social networks could help reach other hard-to-reach populations.
δ-Norm-Based Robust Regression With Applications to Image Analysis

Up to now, various matrix norms (e.g., <inline-formula> <tex-math notation="LaTeX">$ {l_{1}}$ </tex-math></inline-formula>-norm, <inline-formula> <tex-math notation="LaTeX">$ {l_{2}}$ </tex-math></inline-formula>-norm, <inline-formula> <tex-math notation="LaTeX">$ {l_{2,1}}$ </tex-math></inline-formula>-norm, etc.) have been widely leveraged to form the loss function of different regression models, and have played an important role in image analysis. However, the previous regression models adopting the existing norms are sensitive to outliers and, thus, often bring about unsatisfactory results on the heavily corrupted images. This is because their adopted norms for measuring the data residual can hardly suppress the negative influence of noisy data, which will probably mislead the regression process. To address this issue, this paper proposes a novel <inline-formula> <tex-math notation="LaTeX">$ {\delta }$ </tex-math></inline-formula>(delta)-norm to count the nonzero blocks around an element in a vector or matrix, which weakens the impacts of outliers and also takes the structure property of examples into account. After that, we present the <inline-formula> <tex-math notation="LaTeX">$ {\delta }$ </tex-math></inline-formula>-norm-based robust regression (DRR) in which the data examples are mapped to the kernel space and measured by the proposed <inline-formula> <tex-math notation="LaTeX">$ {\delta }$ </tex-math></inline-formula>-norm. By exploring an explicit kernel function, we show that DRR has a closed-form solution, which suggests that DRR can be efficiently solved. To further handle the influences from mixed noise, DRR is extended to a multiscale version. The experimental results on image classification and background modeling datasets validate the superiority of the proposed approach to the existing state-of-the-art robust regression models.
Oxidative and nitrosative stress markers in obsessive–compulsive disorder: a systematic review and meta‐analysis

Obsessive–compulsive disorder (OCD) is a chronic, prevalent, and highly impairing psychiatric illness. Although the pathophysiology of OCD remains unknown, pathways involved in oxidative and nitrosative stress (O&NS) have been implicated. The present study aims to systematically review the literature for quantitative evidence that patients with OCD have altered measures of blood O&NS markers.
Implementing an Integrative Survivorship Program at a Comprehensive Cancer Center: A Multimodal Approach to Life After Cancer.

BACKGROUND This article describes the development of an integrative survivorship program at an urban National Cancer Institute-designated comprehensive cancer center with three closely linked components: a Survivorship Clinic with dedicated staff, a network of Support Services including Wellness, and an Integrative Medicine Program. DEVELOPMENT We first defined the parameters of survivorship care and developed a patient-centric model that determined the optimal timeframes for transitioning these patients from the oncology clinic to a centralized survivorship clinic. Survivorship care includes the development of a survivorship care plan (SCP) for each patient at their initial visit to the program. Quality-of-life assessments are used in real time to guide clinical decision making to referrals to supportive care services, including educational events, expert consultations, and treatment using integrative and complementary therapies, access to legal services, community resource information, and support group activities for cancer survivors and caregivers. Integrative therapies were added to support the needs of this new program, including recruiting a nutritionist and acupuncturist, and developing a yoga, mindfulness, and Reiki program. Population served: As of June 2018, 908 people have accessed our survivorship clinic, receiving a complete clinical assessment and SCP. Patients are routinely referred to support services based on the individual needs and ongoing symptoms from treatment. The majority of referrals are made to acupuncture, Healing Touch or Reiki, nutrition, psychosocial oncology, and yoga. CONCLUSIONS Developing a successful integrative survivorship program requires some essential features, including institutional support, strong leadership, a clear vision of how the clinical program will function, a dedicated team that is willing to do what it takes to get the program off the ground, and clinical oncology champions to refer patients into the program. With the development of this program, this multimodal approach to patient-centric care is maintained throughout the spectrum of care, from diagnosis to survivorship.
Seed Germination in Cistus ladanifer: Heat Shock, Physical Dormancy, Soil Temperatures and Significance to Natural Regeneration

Seeds of Cistus ladanifer experience bursts of germination following fires. The effects of heat shock from 10 °C to 150 °C on seed germination were investigated by final germination plus the number of days required for germination to start and finish, and symmetry of cumulative germination. The occurrence of physical dormancy in C. ladanifer seeds was investigated by a variety of methods, including imbibition, scanning electron microscopy (SEM) and light microscopy, and use of dyes. The significance of responses of C. ladanifer seeds to fires was investigated essentially by abstracting existing literature and by using fire effects models and simulations. Parameters of germination were variously affected by heat treatments—positively in the range 80–100 °C, negatively above 130 °C. Non-dormancy was consistently found in about 30% of seeds but no evidence was obtained to support the existence of physical dormancy in the dormant fraction of C. ladanifer seeds. Two complementary processes seem to be in place in seeds response to fire. A direct fire-driven increase in germination of virtually all seeds in response to the appropriate heat load produced by fire or, in the absence of such heat loads, the germination of the non-dormant fraction provided that above-ground vegetation burns.
Opportunities for genomic selection in American mink: A simulation study

Genomic selection can be considered as an effective tool for developing breeding programs in American mink. However, the genetic gains for economically important traits can be influenced by the accuracy of genomic predictions. The objective of this study was to investigate the prediction accuracies of traditional best linear unbiased prediction (BLUP), multi-step genomic BLUP (GBLUP) and single-step GBLUP (ssGBLUP) methods in American mink using simulated data with different levels of heritability, marker density, training set (TS) sizes and selection designs based on either phenotypic performance or estimated breeding values (EBVs). Under EBV selection design, the accuracy of BLUP predictions was increased by 38% and 44% for h2 = 0.10, 27% and 29% for h2 = 0.20, and 5.8% and 6% for h2 = 0.50 using GBLUP and ssGBLUP methods, respectively. Under phenotypic selection design, the accuracies of prediction by ssGBLUP method were 11.8% and 15.4% higher than those obtained by GBLUP for heritability of 0.10 and 0.20, respectively. However, the efficiency of ssGBLUP and GBLUP was not influenced by selection design at higher level of heritability (h2 = 0.50). Furthermore, higher selection intensity increased the bias of predictions in both pedigree-based and genomic evaluations. Regardless of selection design, TS sizes for GBLUP and ssGBLUP methods should be at least 3000 to achieve more accuracy than using BLUP for heritability of 0.50 and marker density of 10k and 50k. Overall, more accurate predictions were obtained using ssGBLUP method particularly for lowly heritable traits and low density of markers. Our results indicated that TS sizes should be optimized in accordance with heritability level, marker density, selection design and prediction method for genomic selection in American mink. The results provided an initial framework for designing genomic selection in mink breeding programs.
Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish (Danio rerio)

Understanding early gene expression in zebrafish embryos is a prerequisite for developmental biology research. In this study, 1,629,447 polymerase reads were obtained from the unfertilized eggs of zebrafish via full-length transcriptome sequencing using the PacBio RS II platform first. Then, 102,920 unique isoforms were obtained by correction, clustering and comparison with the zebrafish genome. 12,782 genes in the genome were captured, accounting for 39.71% of the all annotated genes. Approximately 62.27% of the 12,782 genes have been alternatively spliced. GO and KEGG annotations revealed that the unfertilized eggs primarily stored genes that participate in RNA processing and nuclear protein complex composition. According to this PacBio data that aligned with the genome, 3,970 fusion genes, 819 ncRNAs, and 84 new transcripts were predicted. Illumina RNA-seq and RT-qPCR detection found that the expression of two new transcripts, PB.5289. 1 and PB.10209. 1, were significantly up-regulated at the 2-cell stage and down-regulated rapidly thereafter, suggesting their involvement in minor ZGA during early embryonic development. This study indicated that the unfertilized eggs of zebrafish may have retained genes directly related to cell division and development to initiate the subsequent development in a limited space and time. On the other hand, NTRs or new transcriptome regions in the genome were discovered, which provided new clues regarding ZGA of MZT during early embryonic development in fish.
Measuring Mental Stress During Otologic Surgery Using Heart Rate Variability Analysis.

OBJECTIVES Healthy individuals have significant beat-to-beat variability in heart rate, and this variability decreases with mental stress. We aim to use heart rate variability (HRV) to objectively compare mental stress levels in otologic surgeons at rest and during key portions of procedures. DESIGN Pilot study. SETTING Operating room and laboratory. PARTICIPANTS Two neurotology fellows performed six mastoidectomy and facial nerve (FN) dissections in the operating room and six in a cadaver lab while continuous electrocardiograms were measured wirelessly. Five-minute samples were recorded during resting, preoperative, mastoidectomy, and FN dissection. Beat-to-beat time intervals were analyzed in time and frequency domains. The standard deviation of normal beat-to-beat intervals (SDNN) and the ratio of low frequency to high frequency power (LF/HF, measure of sympathetic tone) were calculated. Decreases in SDNN and increases in LF/HF indicate elevated mental stress. RESULTS Mean resting SDNN was 43.9 ± 9.2 ms, not statistically different from preoperative SDNN (34.1 ± 8.2 ms, p = 0.13). SDNN decreased during mastoidectomy (29.4 ± 11.7 ms) and FN dissection (22.8 ± 3.1 ms), which was significant compared to preoperative values (p = 0.03). Intraoperative LF/HF increased for FN dissection (6.8 ± 2.6) compared to resting (2.2 ± 0.7, p = 0.004), indicating increased sympathetic tone. Mastoid and FN cadaveric procedures resulted in SDNN of 33.6 ± 3.8 and 32.9 ± 4.7 ms, respectively, not statistically different from preoperative values (p = 0.82 and p = 0.94, respectively). Cadaveric FN dissection did not result in increased LF/HF (2.4 ± 0.9) compared to resting (p = 0.94). CONCLUSIONS Decreased HRV and increased sympathetic tone were observed intraoperatively, indicating high levels of mental stress, particularly with FN dissection. Similar changes were not found during cadaveric dissections.
New York City Panel on Climate Change 2019 Report Chapter 5: Mapping Climate Risk

The mapping work of the NPCC is focused on illustrating spatial climate risk information to inform policy makers, stakeholders, and the public of the distribution of climate risk across the landscape of New York City. Flood risk, overall, has been the primary focus of climate risk, based on a variety of approaches including global climate models, semiempirical studies, literature surveys, expert-opinion, and historic tide gauge and more recently, satellite observations of sea level rise. Maps of potential future flood extents are used to visualize coastal flooding extents at the neighborhood scale and to assess the progression of citywide flood risk throughout the 21st century. The NPCC maps were developed as a tool to illustrate our present understanding of the potential futures for which we need to prepare. This chapter reviews the background, methodology, and limitations of the NPCC3 (and NPCC2) mapping approach and features new citywide maps of mean sea level rise, monthly tidal flooding, and 100-year return period flooding under a high-end scenario of sea level rise. It concludes with a discussion of future mapping efforts and next steps that the NPCC could consider.
Tolerability of FODMAP – reduced diet in irritable bowel syndrome – efficacy, adherence, and body weight course

Abstract Background FODMAP reduced diet (fermentable oligo-, di-, monosaccharide, and polyols) belongs to the established therapy strategies in irritable bowel syndrome (IBS). However, disadvantages of this diet are significant and may lead to weight loss and insufficient patient adherence. Reports from Germany are not available yet. Material and methods In a prospective study, 93 patients with IBS according to Rom III were investigated. Sixty-three patients were recruited for the study and received standardized investigation, informed consent, and structured dietary instructions about the FODMAP reduced diet. Patients complaints were documented by a validated questionnaire and a standardized Lickert scale before and 8 weeks after the start of the diet. Stool characteristics were documented by the Bristol stool form scale. Results Patients adherence was low because 30 patients (47 %) stopped the diet. Of the remaining 33 patients, 36 % (n = 12) developed significant weight loss during the FODMAP therapy. Patients completing the study reported significant global improvement of symptoms in 79 % of cases (abdominal pain 85 %, meteorism 79 %, flatulence 69 %, borbogymi 69 %, nausea 46 %, fatigue 69 %). In addition, the severity of symptoms was significantly reduced. Fourteen patients developed changes of their stool characteristics according to the Bristol stool form scale, 11 of whom improved diarrhea and 3 improved constipation. Conclusion FODMAP reduced diet is an efficient therapy in IBS. However, adherence of the patients is poor and the therapy bears the risk of significant weight loss.