Miracle-dz/UniFAR-FTUs huggingface dataset:
Mice, men and the relatives: cross-species studies underpin innate immunity

The innate immune response is the first line of defence against infection. Germ-line-encoded receptors recognize conserved molecular motifs from both exogenous and endogenous sources. Receptor activation results in the initiation of a pro-inflammatory immune response that enables the resolution of infection. Understanding the inner workings of the innate immune system is a fundamental requirement in the search to understand the basis of health and disease. The development of new vaccinations, the treatment of pathogenic infection, the generation of therapies for chronic and auto-inflammatory disorders, and the ongoing battle against cancer, diabetes and atherosclerosis will all benefit from a greater understanding of innate immunity. The rate of knowledge acquisition in this area has been outstanding. It has been underpinned and driven by the use of model organisms. Information obtained from Drospohila melanogaster, knock-out and knock-in mice, and through the use of forward genetics has resulted in discoveries that have opened our eyes to the functionality and complexity of the innate immune system. With the current increase in genomic information, the range of innate immune receptors and pathways of other species available to study is rapidly increasing, and provides a rich resource to continue the development of innate immune research. Here, we address some of the highlights of cross-species study in the innate immune field and consider the benefits of widening the species-field further.
Exploring the historical earthquakes preceding the giant 1960 Chile earthquake in a time‐dependent seismogenic zone

New documentary findings and available paleoseismological evidence provide both new insights into the historical seismic sequence that ended with the giant 1960 south-central Chile earthquake and relevant information about the region’s seismogenic zone. According to the few available written records, this region was previously struck by earthquakes of varying size in 1575, 1737, and 1837. We expanded the existing compilations of the effects of the two latter using unpublished first-hand accounts found in archives in Chile, Peru, Spain, and New England. We further investigated their sources by comparing the newly unearthed historical data and available paleoseismological evidence with the effects predicted by hypothetical dislocations. The results reveal significant differences in the along-strike and depth distribution of the ruptures in 1737, 1837, and 1960. While the 1737 rupture likely occurred in the northern half of the 1960 region, on a narrow and deep portion of the megathrust, the 1837 rupture occurred mainly in the southern half and slipped over a wide range of depth. Such a wide rupture in 1837 disagrees with the narrow and shallow seismogenic zone currently inferred along this region. If in fact there is now a narrow zone where 200 years ago there was a wider one, it means that the seismogenic zone changes with time, perhaps between seismic cycles. Such change probably explains the evident variability in both size and location of the great earthquakes that have struck this region over the last centuries, as evidenced by written history, and through millennia, as inferred from paleoseismology. Electronic Supplement: First-hand written accounts of the 1737 and 1837 earthquakes, method to compute the tidal level on the 1837 earthquake’s day, hypothesis to explain the minor local effects of the 1837 tsunami, modeling results for each of the 1837 earthquake’s hypothetical sources, and nineteenth-century maps.
Long‐term Effects of 1‐Year Maintenance Training on Physical Functioning and Health Status in Patients With COPD: A Randomized Controlled Study

PURPOSE To examine whether maintenance training (MT) for 1 year improved the long-term effects of a 7-week chronic obstructive pulmonary disease (COPD) rehabilitation program. METHODS After a 7-week outpatient rehabilitation program, 96 patients with COPD were randomized to either an MT group (n = 55) or a control group (n = 41). Both groups were requested to continue unsupervised training at home. The MT group received weekly supervised training the first 6 months, supervised training every second week the next 6 months, and finally no supervised training the last 6 months of the 18-month study period. Primary effect parameters were Endurance Shuttle Walk Test (ESWT) time and health status (St. George's Respiratory Questionnaire, SGRQ). Secondary effect parameters were adherence to supervised training, dropout rates, and hospitalization. RESULTS Compared with the control group, the MT group had significantly better ESWT times at 3 and 6 months (+43.9 seconds; P= .03, and +75.1 seconds; P= .02) and insignificantly higher ESWT time at 12 months (+66.6 seconds; P= .40). SGRQ total score declined gradually after the 7-week program with no difference between the 2 groups, and after 18 months, the score was 1.7 units (95% confidence interval: −0.7 to 4.1) worse than at randomization. There was no difference between the 2 groups regarding dropout rates or hospitalization. DISCUSSION Weekly MT for 12 months improved walking time but had no influence on health-related quality of life or hospital admissions, compared with unsupervised daily training at home. The effect of the MT was closely related to adherence to the program.
Chronic Prostatitis: A Possible Cause of Hematospermia

Purpose While hematospermia is mainly caused by genitourinary inflammatory disorders, very few studies have been published on prostatitis-associated hematospermia (PAH) diagnosed using robust prostatitis evaluation methods. Therefore, we have evaluated the incidence of PAH by using systematic methods for evaluating prostatitis. Materials and Methods We evaluated 37 hematospermia patients from a single hospital over the last five years. We classified the patients into PAH versus hematospermia without any evidence of prostatitis (HWP) by using a NIH-Chronic Prostatitis Symptom Index questionnaire and expressed prostatic secretion studies. Results The mean age was 55.89±14.87 years, and the patients were grouped into two groups: one group had 12 HWP patients and the other 25 PAH patients. PAH patients were further sub-classified: chronic bacterial prostatitis (3 patients), chronic nonbacterial prostatitis (10 patients), prostadynia (7 patients), and asymptomatic prostatitis (5 patients). We found Enterococcus faecalis in the three chronic bacterial prostatitis patients. We could not find any statistically significant difference between the PAH and the HWP groups in terms of the age interval, serum prostate-specific antigen level, and prostate volume. Even though there was no statistically significant difference in the items about urination between the two groups, we found a statistically significant difference in the quality of life (QoL) impact for the patients in this study. Conclusions Two-thirds of the hematospermia patients were associated with some evidence of prostatitis. Further, the patients with PAH revealed poor QoL compared with the patients with HWP. Therefore, we must evaluate the presence of prostatitis in hematospermia patients and alleviate the prostatitis-associated symptoms to improve their QoL.
A nonredundant ternary CAM circuit for network search engines

An optimized Ternary CAM concept is introduced for the hardware search engines in high-speed Internet routers. Our design employs w + 1 RAM bits to store a word of size w, whereas a conventional TCAM needs 2w RAM bits for the same word size. Based on this concept an 8-bit cluster is designed out of 9 SRAM bits, used as the basic building block of our Prefix-CAM (PCAM) structure. Four such clusters merge to store a 32-bit IPv4 prefix, thus, configuring a PCAM suitable for Internet packet forwarding. This PCAM module employs 48% less SRAM cells and a total of 22% less transistors plus 50% less address decode interconnects compared to a conventional TCAM, for equal storage size and equal functionality. We show that PCAM can be employed for multifield packet classification. Other factors, such as lookup speed and power dissipation, are not adversely affected.
First record of the genus Charinus Simon, 1892 from Martinique, Lesser Antilles, with description of a new species (Amblypygi:Charinidae)

The genus CharinusSimon, 1892 is herein recorded for the first time from the Lesser Antillean island of Martinique (a French Overseas Territory), on the basis of two species. One of them occurs in the karstic hill of the southern part of the island and is herein described, supported by a thorough photographic complement. It is compared in detail to all its morphologically closest Antillean relativesand a brief supplementary comment is given on the high-rank taxonomy of the order.
ESTIMATING SOME FEATURES OF NK FITNESS LANDSCAPES

Kauffman and Levin introduced a class of models for the evolution of hereditary systems which they called NK fitness landscapes. Inspired by spinglasses, these models have the attractive feature of being tunable, with regard to both overall size (through the parameter N) and connectivity (through K). There are N genes, each of which exists in two possible alleles [leading to a system indexed by {0, 1} N ]; the fitness score of an allele at a given site is determined by the alleles of K neighboring sites. Otherwise the fitnesses are as simple as possible, namely i.i. d. , and the fitnesses of different sites are simply averaged. Much attention has been focused on these fitness landscapes as paradigms for investigating the interaction between size and complexity in making evolution possible. In particular, the effect of the interaction parameter K on the height of the global maximum and the heights of local maxima has attracted considerable interest, as well as the behavior of a “hill-climbing” walk from a random starting point. Nearly all of this work has relied on simulations, not on rigorous mathematics. In this paper, some asymptotic features of NK fitness landscapes are reduced to questions about eigenvalues and Lyapunov exponents. When K is fixed, the expected number of local maxima grows exponentially with N at a rate depending on the top eigenvalue of a kernel derived from the distribution of the fitnesses, and the average height of a local maximum converges to a value determined by the corresponding eigenfunction. The global maximum converges in probability as N →∞ to a constant given by the top Lyapunov exponent for a system of i.i. d. max-plus random matrices, and this constant is nondecreasing with K. Various such quantities are computed for certain special cases when K is small, and these calculations can, in principle, be extended to larger K.
Preconditioning L6 Muscle Cells with Naringin Ameliorates Oxidative Stress and Increases Glucose Uptake

Enhanced oxidative stress contributes to pathological changes in diabetes and its complications. Thus, strategies to reduce oxidative stress may alleviate these pathogenic processes. Herein, we have investigated Naringin mediated regulation of glutathione (GSH) & intracellular free radical levels and modulation of glucose uptake under oxidative stress in L6 cell lines. The results from the study demonstrated a marked decrease in glutathione with a subsequent increase in free radical levels, which was reversed by the pretreatment of Naringin. We also observed that the increased malondialdehyde level, the marker of lipid peroxidation on induction of oxidative stress was retrieved on Naringin pretreatment. Addition of Naringin (100 μM) showed approximately 40% reduction in protein glycation in vitro. Furthermore, we observed a twofold increase in uptake of fluorescent labeled glucose namely 2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose (2 - NBDG) on Naringin treatment in differentiated L6 myoblast. The increased uptake of 2-NBDG by L6 myotubes may be attributed due to the enhanced translocation of GLUT4. Our results demonstrate that Naringin activate GSH synthesis through a novel antioxidant defense mechanism against excessive Reactive Oxygen Species (ROS) production, contributing to the prevention of oxidative damage in addition to its effect on glycemic control.
An Appraisal of the Management of Ectopic Pregnancy in a Nigerian Tertiary Hospital

Background: Ectopic pregnancy has remained a significant cause of maternal morbidity and mortality especially in the sub Saharan Africa. A periodic appraisal of its management is paramount. Aim: To determine the incidence and associated risk factors, for ectopic pregnancy, review available treatment modalities and suggest interventions to reduce its prevalence, morbidity and mortality. Materials and Methods: A cross sectional study with retrolective data collection of all cases of ectopic pregnancy managed in Nnamdi Azikiwe University Teaching Hospital, Nnewi, south-east Nigeria between 1st January, 2002 and 31st December, 2011 was undertaken. Analysis was carried out using Epi-info 2008 version 3.5. 1. Results: During the study period, there were a total 98 cases of ectopic pregnancies out of 8,811 deliveries and 1884 gynecological admissions, giving an incidence of 0.9% of all attendants or 1 in 90 deliveries and 5.2% of all gynecological admissions. Only 94.9% (93/98) case files were retrieved and were used in the final analysis. The mean age of the patients was 30.1 (0.7) years while the mean gestational age at presentations was 7.4 weeks. Previous induced abortion, 37.5% (36/93) was the commonest associated risk factor, followed by pelvic infections, 35.5% (33/93). The recurrence rate was 6.5% (6/93). Majority, 80.6% (75/93) presented with abdominal pain and 35.8% (33/93) presented with vaginal bleeding. Up to 88.2% (82/93) had salpingectomy while only 2.5% (2/93) were successfully managed medically with methotrexate therapy following diagnosis with transvaginal ultrasound Missed diagnosis of ectopic pregnancy occurred in 16.1% (15/93). There was no maternal death. Conclusion: Ectopic pregnancy has remained an important gynecological condition in our center. The common identifiable risk factors were induced abortion and pelvic infection. Early first trimester transvaginal ultrasound should be offered to all women for early diagnosis.
Ubiquitin-Specific Protease 14 Negatively Regulates Toll-Like Receptor 4-Mediated Signaling and Autophagy Induction by Inhibiting Ubiquitination of TAK1-Binding Protein 2 and Beclin 1

Ubiquitin-specific protease 14 (USP14), one of three proteasome-associated deubiquitinating enzymes, has multifunctional roles in cellular context. Here, we report a novel molecular mechanism and function of USP14 in regulating autophagy induction and nuclear factor-kappa B (NF-κB) activation induced by toll-like receptor (TLR) 4 (TLR4). USP14 interacted with tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and interrupted the association of Beclin 1 with TRAF6, leading to inhibition of TRAF6-mediated ubiquitination of Beclin 1. Reduced expression of USP14 in USP14-knockdown (USP14KD) THP-1 cells enhanced autophagy induction upon TLR4 stimulation as shown by the increased conversion of cytosolic LC3-I to membrane-bound LC3-II. Moreover, USP14KD human breast carcinoma MDA-MB-231 cells and USP14KD human hepatic adenocarcinoma SK-HEP-1 cells showed increased cell migration and invasion, indicating that USP14 is negatively implicated in the cancer progression by the inhibition of autophagy induction. Furthermore, we found that USP14 interacted with TAK1-binding protein (TAB) 2 protein and induced deubiquitination of TAB 2, a key factor in the activation of NF-κB. Functionally, overexpression of USP14 suppressed TLR4-induced activation of NF-κB. In contrast, USP14KD THP-1 cells showed enhanced activation of NF-κB, NF-κB-dependent gene expression, and production of pro-inflammatory cytokines such as IL-6, IL-1β, and tumor necrosis factor-α. Taken together, our data demonstrate that USP14 can negatively regulate autophagy induction by inhibiting Beclin 1 ubiquitination, interrupting association between TRAF6 and Beclin 1, and affecting TLR4-induced activation of NF-κB through deubiquitination of TAB 2 protein.
Advance Directives in Community Patients With Heart Failure

Background— Although it is recommended that all patients with heart failure (HF) have advance directives (AD) in place before the end of life is imminent, the use of AD in HF has not been well studied. Methods and Results— We enrolled consecutive Olmsted County residents presenting with HF from October 2007 through October 2011 into a longitudinal study. Information from AD completed before enrollment and hospitalizations in the month before death were abstracted. Among 608 patients (mean age, 74.0 years; 54.9% men; 65.3%; New York Heart Association functional class 3 or 4), 164 (27.0%) patients died after a mean follow-up of 1.8 years. At enrollment, only 249 (41.0%) patients had an AD. Although most AD appointed a proxy decision-maker (90.4%), less than half addressed wishes regarding use of cardiopulmonary resuscitation (41.4%), mechanical ventilation (38.6%), or hemodialysis (10.0%) at the end of life. The independent predictors of AD completion were older age (adjusted odds ratio [OR] per 10-year increase, 1.82; 95% confidence interval [CI], 1.51–2.20), malignancy (OR, 1.58; 95% CI, 1.05–2.37), and renal dysfunction (OR for estimated glomerular filtration rate <60 mL/min 1.55; 95% CI, 1.05–2.29). At the end of life, patients with AD specifying limits in the aggressiveness of care less frequently received mechanical ventilation (OR, 0.26; 95% CI, 0.07–0.88), with a trend toward decreased intensive care unit admission (OR, 0.45; 95% CI, 0.16–1.29). Conclusions— Despite a high mortality rate, over half of patients with HF do not have an AD, and existing AD fail to address important end-of-life medical decisions.
Terminology and quantification of environmental heterogeneity in species‐richness research

Spatial environmental heterogeneity (EH) is an important driver of species diversity, and its influence on species richness has been analysed for numerous taxa, in diverse ecological settings, and over a large range of spatial scales. The variety and ambiguity of concepts and terminology, however, have hampered comparisons among studies. Based on a systematic literature survey of 192 studies including 1148 data points, we provide an overview of terms and measures related to EH, and the mechanisms that relate EH to species richness of plants and animals in terrestrial systems. We identify 165 different measures used to quantify EH, referred to by more than 350 measure names. We classify these measures according to their calculation method and subject area, finding that most studies have analysed heterogeneity in land cover, topography, and vegetation, whereas comparatively few studies have focused on climatic or soil EH. Overall, elevation range emerged as the most frequent measure in our dataset. We find that there is no consensus in the literature about terms (such as ‘habitat diversity’ or ‘habitat complexity’), their meanings and associated quantification methods. More than 100 different terms have been used to denote EH, with largely imprecise delimitations. We reveal trends in use of terms and quantification with respect to spatial scales, study taxa, and locations. Finally, we discuss mechanisms involved in EH–richness relationships, differentiating between effects on species coexistence, persistence, and diversification. This review aims at guiding researchers in their selection of heterogeneity measures. At the same time, it shows the need for precise terminology and avoidance of ambiguous synonyms to enhance understanding and foster among‐study comparisons and synthesis.
Rhodenigma contortum, an obscure new genus and species of Rhodogorgonales (Rhodophyta) from Western Australia

An unknown microscopic, branched filamentous red alga was isolated into culture from coral fragments collected in Coral Bay, Western Australia. It grew well unattached or attached to glass with no reproduction other than fragmentation of filaments. Cells of some branch tips became slightly contorted and digitated, possibly as a substrate‐contact‐response seen at filament tips of various algae. Attached multicellular compact disks on glass had a very different cellular configuration and size than the free filaments. In culture the filaments did not grow on or in coral fragments. Molecular phylogenies based on four markers (rbcL, cox1, 18S, 28S) clearly showed it belongs to the order Rhodogorgonales, as a sister clade of Renouxia. Based on these results, the alga is described as the new genus and species Rhodenigma contortum in the Rhodogorgonaceae. It had no morphological similarity to either of the other genera in Rhodogorgonaceae and illustrates the unknown diversity in cryptic habitats such as tropical coral rubble.
Evolving Growth Prospects?: Assessing the State of the South in the Global Economy

Despite rapid population growth, parts of the southern United States often lag the nation in measures of productivity, wages, and wealth. This paper revisits evaluation of Southern economic readiness for the global era in order to assess the region's contemporary adaptation to the global economy. Moreover, it explores the geographies of economic evolution within the South by measuring relative changes in population, productivity, poverty, education, and foreign direct investment. With the exception of population growth and high school graduation rates, these analyses suggest that the region has regressed relative to the nation in many measures. The findings intimate that this economic decline could be tied to region-wide policy regimes that are reliant on maintaining low wages and present a structural obstacle to economic evolution.Resumen:A pesar del rápido crecimiento de la población, algunas partes del sur de los Estados Unidos a menudo se quedan rezagadas con medidas de productividad, salarios y riqueza. Este documento revisa la evaluación de Glasmeier y Leichenko de 1996 sobre la preparación económica del Sur para la era global con el fin de evaluar la adaptación contemporánea de la región a la economía global. Además, explora las geografías de la evolución económica en el Sur, midiendo los cambios relativos en la población, la productividad, la pobreza, la educación y la inversión extranjera directa. Con la excepción del crecimiento de la población y las tasas de graduación de la escuela secundaria, estos análisis sugieren que la región ha retrocedido en relación con la nación en muchas medidas. Los hallazgos indican que este declive económico podría estar vinculado a regímenes de políticas regionales que dependen de mantener bajos salarios y constituir un obstáculo estructural a la evolución económica.
The Population and Evolutionary Dynamics of Vibrio cholerae and Its Bacteriophage: Conditions for Maintaining Phage-Limited Communities

Although bacteriophage have been reported to be the most abundant organisms on earth, little is known about their contribution to the ecology of natural communities of their host bacteria. Most importantly, what role do these viral parasitoids play in regulating the densities of bacterial populations? To address this question, we use experimental communities of Vibrio cholerae and its phage in continuous culture, and we use mathematical models to explore the population dynamic and evolutionary conditions under which phage, rather than resources, will limit the densities of these bacteria. The results of our experiments indicate that single species of bacterial viruses cannot maintain the density of V. cholerae populations at levels much lower than that anticipated on the basis of resources alone. On the other hand, as few as two species of phage can maintain these bacteria at densities more than two orders of magnitude lower than the densities of the corresponding phage-free controls for extensive periods. Using mathematical models and short-term experiments, we explore the population dynamic processes responsible for these results. We discuss the implications of this experimental and theoretical study for the population and evolutionary dynamics of natural populations of bacteria and phage.