To Transformers and Beyond: Large Language Models for the Genome

In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool for tackling complex computational challenges. This review focuses on the transformative role of Large Language Models (LLMs), which are mostly based on the transformer architecture, in genomics. Building on the foundation of traditional convolutional neural networks and recurrent neural networks, we explore both the strengths and limitations of transformers and other LLMs for genomics. Additionally, we contemplate the future of genomic modeling beyond the transformer architecture based on current trends in research. The paper aims to serve as a guide for computational biologists and computer scientists interested in LLMs for genomic data. We hope the paper can also serve as an educational introduction and discussion for biologists to a fundamental shift in how we will be analyzing genomic data in the future

Spectral Energy Distributions of Local Luminous And Ultraluminous Infrared Galaxies

Luminous and ultraluminous infrared galaxies ((U)LIRGs) are the most extreme star forming galaxies in the universe. The local (U)LIRGs provide a unique opportunity to study their multi-wavelength properties in detail for comparison to their more numerous counterparts at high redshifts. We present common large aperture photometry at radio through X-ray wavelengths, and spectral energy distributions (SEDs) for a sample of 53 nearby LIRGs and 11 ULIRGs spanning log (LIR/Lsun) = 11.14-12.57 from the flux-limited Great Observatories All-sky LIRG Survey (GOALS). The SEDs for all objects are similar in that they show a broad, thermal stellar peak and a dominant FIR thermal dust peak, where nuLnu(60um) / nuLnu(V) increases from ~2-30 with increasing LIR. When normalized at IRAS-60um, the largest range in the luminosity ratio, R(lambda)=log[nuLnu(lambda)/nuLnu(60um)] observed over the full sample is seen in the Hard X-rays (HX=2-10 keV). A small range is found in the Radio (1.4GHz), where the mean ratio is largest. Total infrared luminosities, LIR(8-1000um), dust temperatures, and dust masses were computed from fitting thermal dust emission modified blackbodies to the mid-infrared (MIR) through submillimeter SEDs. The new results reflect an overall ~0.02 dex lower luminosity than the original IRAS values. Total stellar masses were computed by fitting stellar population synthesis models to the observed near-infrared (NIR) through ultraviolet (UV) SEDs. Mean stellar masses are found to be log(M/Msun) = 10.79+/-0.40. Star formation rates have been determined from the infrared (SFR_IR~45Msun/yr) and from the monochromatic UV luminosities (SFR_UV~1.3Msun/yr), respectively. Multiwavelength AGN indicators have be used to select putative AGN: about 60% of the ULIRGs would have been classified as an AGN by at least one of the selection criteria.Comment: 39 pages, including 12 figures and 11 tables; accepted for publication in ApJ

Mercury from chlor-alkali plants: measured concentrations in food product sugar

Mercury cell chlor-alkali products are used to produce thousands of other products including food ingredients such as citric acid, sodium benzoate, and high fructose corn syrup. High fructose corn syrup is used in food products to enhance shelf life. A pilot study was conducted to determine if high fructose corn syrup contains mercury, a toxic metal historically used as an anti-microbial. High fructose corn syrup samples were collected from three different manufacturers and analyzed for total mercury. The samples were found to contain levels of mercury ranging from below a detection limit of 0.005 to 0.570 micrograms mercury per gram of high fructose corn syrup. Average daily consumption of high fructose corn syrup is about 50 grams per person in the United States. With respect to total mercury exposure, it may be necessary to account for this source of mercury in the diet of children and sensitive populations

Strong evidence that the common variant S384F in BRCA2 has no pathogenic relevance in hereditary breast cancer

INTRODUCTION: Unclassified variants (UVs) of unknown clinical significance are frequently detected in the BRCA2 gene. In this study, we have investigated the potential pathogenic relevance of the recurrent UV S384F (BRCA2, exon 10). METHODS: For co-segregation, four women from a large kindred (BN326) suffering from breast cancer were analysed. Moreover, paraffin-embedded tumours from two patients were analysed for loss of heterozygosity. Co-occurrence of the variant with a deleterious mutation was further determined in a large data set of 43,029 index cases. Nature and position of the UV and conservation among species were evaluated. RESULTS: We identified the unclassified variant S384F in three of the four breast cancer patients (the three were diagnosed at 41, 43 and 57 years of age). One woman with bilateral breast cancer (diagnosed at ages 32 and 50) did not carry the variant. Both tumours were heterozygous for the S384F variant, so loss of the wild-type allele could be excluded. Ser384 is not located in a region of functional importance and cross-species sequence comparison revealed incomplete conservation in the human, dog, rodent and chicken BRCA2 homologues. Overall, the variant was detected in 116 patients, five of which co-occurred with different deleterious mutations. The combined likelihood ratio of co-occurrence, co-segregation and loss of heterozygosity revealed a value of 1.4 × 10(-8 )in favour of neutrality of the variant. CONCLUSION: Our data provide conclusive evidence that the S384F variant is not a disease causing mutation

Hope in action—facing cardiac death: A qualitative study of patients with life-threatening disease

Coping with existential challenges is important when struck by serious disease, but apart from cancer and palliative care little is known about how patients deal with such issues and maintain hope. To explore how patients with life-threatening heart disease experience hope when coping with mortality and other existential challenges, we conducted a qualitative study with semi-structured interviews. We made a purposive sample of 11 participants (26–88 years) who had experienced life-threatening disease: eight participants with serious heart disease, two with cancer, and one with severe chronic obstructive pulmonary disease. Analysis was by systematic text condensation. The findings showed that hope could enhance coping and diminish existential distress when patients were confronted with mortality and other existential challenges. Hope was observed as three types of dynamic work: to shift perception of mortality from overwhelming horror toward suppression or peaceful acceptance, to foster reconciliation instead of uncertainty when adapting to the new phase of life, and to establish go-ahead spirit instead of resignation as their identity. Meaning of life could, hence, be sustained in spite of serious threats to the persons' future, everyday life, and self-conception. The work of hoping could be supported or disturbed by relationships with family, friends, and health care professionals. Hope can be regarded as an active, dynamic state of existential coping among patients with life-threatening disease. Physicians may support this coping and thereby provide personal growth and alleviation of existential distress by skillfully identifying, acknowledging, and participating in the work of hoping performed by the patient

A Coordinated Effort to Manage Soybean Rust in North America: A Success Story in Soybean Disease Monitoring

Existing crop monitoring programs determine the incidence and distribution of plant diseases and pathogens and assess the damage caused within a crop production region. These programs have traditionally used observed or predicted disease and pathogen data and environmental information to prescribe management practices that minimize crop loss (3,69). Monitoring programs are especially important for crops with broad geographic distribution or for diseases that can cause rapid and great economic losses. Successful monitoring programs have been developed for several plant diseases, including downy mildew of cucurbits, Fusarium head blight of wheat, potato late blight, and rusts of cereal crops (13,36,51,80)

Herbal supplements in the print media: communicating benefits and risks

Background The rise in use of food supplements based on botanical ingredients (herbal supplements) is depicted as part of a trend empowering consumers to manage their day-to-day health needs, which presupposes access to clear and accurate information to make effective choices. Evidence regarding herbal supplement efficacy is extremely variable so recent regulations eliminating unsubstantiated claims about potential effects leave producers able to provide very little information about their products. Medical practitioners are rarely educated about herbal supplements and most users learn about them via word-of-mouth, allowing dangerous misconceptions to thrive, chief among them the assumption that natural products are inherently safe. Print media is prolific among the information channels still able to freely discuss herbal supplements. Method This study thematically analyses how 76 newspaper/magazine articles from the UK, Romania and Italy portray the potential risks and benefits of herbal supplements. Results Most articles referenced both risks and benefits and were factually accurate but often lacked context and impartiality. More telling was how the risks and benefits were framed in service of a chosen narrative, the paucity of authoritative information allowing journalists leeway to recontextualise herbal supplements in ways that serviced the goals and values of their specific publications and readerships. Conclusion Providing sufficient information to empower consumers should not be the responsibility of print media, instead an accessible source of objective information is required.</p

Interventions aimed at increasing research use in nursing: a systematic review

<p>Abstract</p> <p>Background</p> <p>There has been considerable interest recently in developing and evaluating interventions to increase research use by clinicians. However, most work has focused on medical practices; and nursing is not well represented in existing systematic reviews. The purpose of this article is to report findings from a systematic review of interventions aimed at increasing research use in nursing.</p> <p>Objective</p> <p>To assess the evidence on interventions aimed at increasing research use in nursing.</p> <p>Methods</p> <p>A systematic review of research use in nursing was conducted using databases (Medline, CINAHL, Healthstar, ERIC, Cochrane Central Register of Controlled Trials, and Psychinfo), grey literature, ancestry searching (Cochrane Database of Systematic Reviews), key informants, and manual searching of journals. Randomized controlled trials and controlled before- and after-studies were included if they included nurses, if the intervention was explicitly aimed at increasing research use or evidence-based practice, and if there was an explicit outcome to research use. Methodological quality was assessed using pre-existing tools. Data on interventions and outcomes were extracted and categorized using a pre-established taxonomy.</p> <p>Results</p> <p>Over 8,000 titles were screened. Three randomized controlled trials and one controlled before- and after-study met the inclusion criteria. The methodological quality of included studies was generally low. Three investigators evaluated single interventions. The most common intervention was education. Investigators measured research use using a combination of surveys (three studies) and compliance with guidelines (one study). Researcher-led educational meetings were ineffective in two studies. Educational meetings led by a local opinion leader (one study) and the formation of multidisciplinary committees (one study) were both effective at increasing research use.</p> <p>Conclusion</p> <p>Little is known about how to increase research use in nursing, and the evidence to support or refute specific interventions is inconclusive. To advance the field, we recommend that investigators: (1) use theoretically informed interventions to increase research use, (2) measure research use longitudinally using theoretically informed and psychometrically sound measures of research use, as well as, measuring patient outcomes relevant to the intervention, and (3) use more robust and methodologically sound study designs to evaluate interventions. If investigators aim to establish a link between using research and improved patient outcomes they must first identify those interventions that are effective at increasing research use.</p