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Medical research frequently relies on Cox regression to analyze the survival distribution of cancer patients. Nonetheless, in specific scenarios, neural networks hold the potential to serve as a robust alternative. In this study, we aim to scrutinize the effectiveness of Cox regression and neural network models in assessing the survival outcomes of patients who have undergone treatment for colorectal cancer. We conducted a retrospective study on 284 colorectal cancer patients who underwent surgery at Imam Khomeini clinic in Hamadan between 2001 and 2017. The data was used to train both Cox regression and neural network models, and their predictive accuracy was compared using diagnostic measures such as sensitivity, specificity, positive predictive value, accuracy, negative predictive value, and area under the receiver operating characteristic curve. The analyses were performed using STATA 17 and R4.0.4 software. The study revealed that the best neural network model had a sensitivity of 74.5% (95% CI 61.0–85.0), specificity of 83.3% (65.3–94.4), positive predictive value of 89.1% (76.4–96.4), negative predictive value of 64.1% (47.2–78.8), AUC of 0.79 (0.70–0.88), and accuracy of 0.776 for death prediction. For recurrence, the best neural network model had a sensitivity of 88.1% (74.4–96.0%), specificity of 83.7% (69.3–93.2%), positive predictive value of 84.1% (69.9–93.4%), negative predictive value of 87.8% (73.8–95.9%), AUC of 0.86 (0.78–0.93), and accuracy of 0.859. The Cox model had comparable results, with a sensitivity of 73.6% (64.8–81.2) and 85.5% (78.3–91.0), specificity of 89.6% (83.8–93.8) and 98.0% (94.4–99.6), positive predictive value of 84.0% (75.6–90.4) and 97.4% (92.6–99.5), negative predictive value of 82.0% (75.6–90.4) and 88.8% (0.83–93.1), AUC of 0.82 (0.77–0.86) and 0.92 (0.89–0.95), and accuracy of 0.88 and 0.92 for death and recurrence prediction, respectively. In conclusion, the study found that both Cox regression and neural network models are effective in predicting early recurrence and death in patients with colorectal cancer after curative surgery. The neural network model showed slightly better sensitivity and negative predictive value for death, while the Cox model had better specificity and positive predictive value for recurrence. Overall, both models demonstrated high accuracy and AUC, indicating their usefulness in predicting these outcomes.

Pollinator nutritional ecology provides insights into plant–pollinator interactions, coevolution, and the restoration of declining pollinator populations. Bees obtain their protein and lipid nutrient intake from pollen, which is essential for larval growth and development as well as adult health and reproduction. Our previous research revealed that pollen protein to lipid ratios (P:L) shape bumble bee foraging preferences among pollen host-plant species, and these preferred ratios link to bumble bee colony health and fitness. Yet, we are still in the early stages of integrating data on P:L ratios across plant and bee species. Here, using a standard laboratory protocol, we present over 80 plant species’ protein and lipid concentrations and P:L values, and we evaluate the P:L ratios of pollen collected by three bee species. We discuss the general phylogenetic, phenotypic, behavioral, and ecological trends observed in these P:L ratios that may drive plant–pollinator interactions; we also present future research questions to further strengthen the field of pollination nutritional ecology. This dataset provides a foundation for researchers studying the nutritional drivers of plant–pollinator interactions as well as for stakeholders developing planting schemes to best support pollinators.

Overlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays, and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1.

There are many non-pathogenic viruses that are maintained in a persistent lifestyle in plants. Plant persistent viruses are widespread, replicating in their hosts for many generations. The roles of plant persistent viruses have not been studied thoroughly, but their very long-term relationships with their hosts, and their high level of vertical transmission imply beneficial interactions. So far, Endornaviridae is the only family with a single-stranded RNA genome, containing one large open reading frame. Bell pepper endornavirus (BPEV), Hot pepper endornavirus, Capsicum frutescens endornavirus 1 (CFEV 1) have been identified from peppers. Peppers are native to Central and South America, and as domesticated plants human selection accelerated their evolution. Using a collection of 97 different peppers the evolution of pepper persistent viruses was studied. The evolution of endornaviruses in different peppers was investigated using two fragments from the viral helicase (Hel) and RNA dependent RNA polymerase (RdRp) domains. In addition, by using single nucleotide polymorphisms the pepper host populations and phylogenies were analyzed. The endornaviruses phylogeny was correlated with its Capsicum species host. In this study BPEV was limited to C. annuum species, and the RdRp and Hel phylogenies identified two clades that correlated with the host pungency. No C. annuum infected with CFEV 1 was found in this study, but the CFEV 1 RdRp fragment was recovered from C.chinense, C. frutescens, and C.bacccutum and C. pubescens.Partitiviridae is the most common persistent virus family in wild plants. Jalapeño and Hungarian Wax peppers (Capsicum annuum) have been reported with Pepper cryptic virus 1 (PCV 1) and Pepper cryptic virus 2 (PCV 2), respectively. Both viruses belong to the genus Deltapartitivirus from Partitiviridae family. The evolution of PCV 1 and PCV 2 was investigated using the RdRp and coat protein of both viruses. Both viruses were detected in cultivated and wild peppers. It is shown that these viruses have a remarkably slow evolution rate in comparison with acute RNA viruses. This might be correlated with the strong purifying selection related to the lifestyle of theses viruses, or the replication strategies in double stranded RNA viruses, that use a stamping machine mode of replication.Finally, some potential beneficial effects of persistent virus were examined. In wild plants partitivirus infection decreased the likelihood of acute virus infection. I compared the effect of odor cues from PCV 1 infected (J+) and virus free (J-) Jalapeño pepper on the aphid Myzus periscae, a common vector of acute plant viruses. Pairwise preference experiments showed a stark contrast to insect-plant interactions in acute virus infections: virus infected plants deterred aphids. The acute plant virus Cucumber mosaic virus (CMV) manipulates its host's volatile emission to attract aphid vectors and facilitate its transmission. Volatiles of J+ and J- CMV infected plants were more attractive to aphids than J+ and J- mock inoculated plants. However, in pairwise preference between J+ CMV- and J- CMV-infected plants, aphids preferred the J- CMV volatile blend. Also, aphid fecundity on J+ and J- plants was measured as an indicator for the effect of PCV 1 on host quality for aphids. Aphid reproduction on J+ plants was more than two fold lower than J- plants. This study demonstrates a beneficial relationship between PCV 1 and Jalapeño plants by protecting the plants from the vector of acute viruses. In addition, the effect of PCV 1 on the Jalapeño's developmental growth was tested by measuring the average time required for seed germination, emergence of first true leaf, first open flower and dried biomass of plants. PCV 1 showed no significant effect on the developmental growth of Jalapeño plants.

Overlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179046 * https://github.com/jferna10/EnvPaper/

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.

This study aimed to investigate the prevalence and pattern of injecting drug use (IDU) in Iranian incarcerated people one month before their imprisonment. This cross-sectional study used data from the national Bio-Behavioral Surveillance Surveys conducted from a random sample of people incarcerated in 33 prisons covering the major geographical areas of Iran in 2017 ( n  = 5,785). A multivariable logistic regression model was used to determine factors related to IDU one month before imprisonment. The lifetime prevalence of IDU among Iranian incarcerated people was 12.2% (95% confidence interval [CI] 11.4, 13.1), of whom 19.2% (95% CI16.3, 22.3) injected in the month before imprisonment. Among incarcerated people with a lifetime history of IDU, the average age at which they started IDU was 24.5 ± 5.9 years, and the mean injection duration was 36.8 months (95% CI 33.5, 40.1). Friends were the initial influence for starting IDU in 67.7% of cases. Additionally, 58.6% of incarcerated people with a history of IDU used a new syringe/needle for injections in the month before imprisonment. Participants over 40 years old were less likely to inject in the month before incarceration than the 18-to-29-year age group (adjusted odds ratio [AOR] 0.37, 95% CI 0.19, 0.73). A history of previous imprisonment (AOR 2.17, 95% CI 1.27, 3.70) and having a tattoo (AOR 1.75, 95% CI 1.15, 2.68) showed significant positive associations with IDU in the month before imprisonment. The study found that one in eight persons detained in Iran had a history of IDU, of whom one in five injected in the month before incarceration with higher rates among persons with younger age, tattoos, and previous incarceration. Implementing targeted prevention programs within prisons, including better access to rehabilitation and needle exchange programs, is recommended to reduce the risks of infectious disease transmission including HIV and HCV.

Objective: Transplants of multipotent stem cells have been shown to have a neuroprotectiveeffect after central nervous system injury. The bulge region of the hair follicle hasbeen reported as a putative source of hair follicle stem cells (HFSC) for many years;however, few studies have documented the properties of bulge derived cells in vitro untilnow. This study was conducted to isolate and culture bulge cells from rat hair folliclesand to determine the morphological and biological features of the cultured cells.Materials and Methods: The bulge region of the rat whisker was isolated and culturedin Dulbecco's modified eagle medium: nutrient mixture F-12 (DMEM/F12) supplementedwith epidermal growth factor (EGF), cholera toxin. Dissociated bulge stemcells were differentiated on coated substrates together with NT-3. The morphologicaland biological features of cultured bulge cells were observed by light microscopy andimmunocytochemistry methods.Results: Our results showed that newly proliferated cells could be observed on the 4thday after explantation. The expression of a neural progenitor marker, nestin, was seenbefore differentiation of the bulge cells. The differentiated cells expressed βIII-Tubulinand RIP, which are the markers of neural and glial lineages.Conclusion: The results indicated that the bulge cells cultured from the rat hair folliclehad the characteristics of stem cells and could differentiate into neural and glial lineages.