ProtoCode: Leveraging large language models (LLMs) for automated generation of machine-readable PCR protocols from scientific publications.

Protocol standardization and sharing are crucial for reproducibility in life sciences. In spite of numerous efforts for standardized protocol description, adherence to these standards in literature remains largely inconsistent. Curation of protocols are especially challenging due to the labor intensive process, requiring expert domain knowledge of each experimental procedure. Recent advancements in Large Language Models (LLMs) offer a promising solution to interpret and curate knowledge from complex scientific literature. In this work, we develop ProtoCode, a tool leveraging fine-tune LLMs to curate protocols into intermediate representation formats which can be interpretable by both human and machine interfaces. Our proof-of-concept, focused on polymerase chain reaction (PCR) protocols, retrieves information from PCR protocols at an accuracy ranging 69-100 % depending on the information content. In all tested protocols, we demonstrate that ProtoCode successfully converts literature-based protocols into correct operational files for multiple thermal cycler systems. In conclusion, ProtoCode can alleviate labor intensive curation and standardization of life science protocols to enhance research reproducibility by providing a reliable, automated means to process and standardize protocols. ProtoCode is freely available as a web server at https://curation.taxila.io/ProtoCode/.

IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.

The increasing availability of single-cell RNA-sequencing (scRNA-seq) data from various developmental systems provides the opportunity to infer gene regulatory networks (GRNs) directly from data. Herein we describe IQCELL, a platform to infer, simulate, and study executable logical GRNs directly from scRNA-seq data. Such executable GRNs allow simulation of fundamental hypotheses governing developmental programs and help accelerate the design of strategies to control stem cell fate. We first describe the architecture of IQCELL. Next, we apply IQCELL to scRNA-seq datasets from early mouse T-cell and red blood cell development, and show that the platform can infer overall over 74% of causal gene interactions previously reported from decades of research. We will also show that dynamic simulations of the generated GRN qualitatively recapitulate the effects of known gene perturbations. Finally, we implement an IQCELL gene selection pipeline that allows us to identify candidate genes, without prior knowledge. We demonstrate that GRN simulations based on the inferred set yield results similar to the original curated lists. In summary, the IQCELL platform offers a versatile tool to infer, simulate, and study executable GRNs in dynamic biological systems.

Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer's disease.

BACKGROUND: Identifying novel therapeutic targets is crucial for the successful development of drugs. However, the cost to experimentally identify therapeutic targets is huge and only approximately 400 genes are targets for FDA-approved drugs. As a result, it is inevitable to develop powerful computational tools that can identify potential novel therapeutic targets. Fortunately, the human protein-protein interaction network (PIN) could be a useful resource to achieve this objective. METHODS: In this study, we developed a deep learning-based computational framework that extracts low-dimensional representations of high-dimensional PIN data. Our computational framework uses latent features and state-of-the-art machine learning techniques to infer potential drug target genes. RESULTS: We applied our computational framework to prioritize novel putative target genes for Alzheimer's disease and successfully identified key genes that may serve as novel therapeutic targets (e.g., DLG4, EGFR, RAC1, SYK, PTK2B, SOCS1). Furthermore, based on these putative targets, we could infer repositionable candidate-compounds for the disease (e.g., tamoxifen, bosutinib, and dasatinib). CONCLUSIONS: Our deep learning-based computational framework could be a powerful tool to efficiently prioritize new therapeutic targets and enhance the drug repositioning strategy.

Influence of age and gender on the pulse waveform in optic nerve head circulation in healthy men and women.

The influences of age and gender differences on the pulse waveform in the optic nerve head (ONH) in healthy adults, using laser speckle flowgraphy (LSFG) were evaluated. We studied 908 healthy subjects (men = 701, age: 50.0 ± 9.1, women = 208, age: 49.8 ± 9.5, p = 0.76), evaluating these pulse waveform parameters: the blowout score (BOS), blowout time (BOT), acceleration time index (ATI), and the rising and falling rates. The parameters were analyzed separately for the tissue, vessels, and throughout the optic nerve head (All). All parameters were compared between genders. We investigated which independent factors for the pulse waveform in the ONH is most strongly correlated with age. All sections of the BOS, BOT, ATI, and falling rate showed a significant gender difference. A univariate regression analysis revealed that BOT-Tissue showed the strongest correlation with age (r = -0.51). The factors contributing independently to the BOT-Tissue were gender, age, heart rate, mean arterial blood pressure, pulse pressure, spherical refraction, and estimated glomerular filtration rate. Among the subjects aged >41 years, the chronological changes of BOT-Tissue in the women were significantly lower than those in the men. We concluded that the pulse waveform in the ONH has clear differences between the genders and shows chronological changes.

The influences of gender and aging on optic nerve head microcirculation in healthy adults.

Potential differences in the nature of the influences of aging and gender on the optic nerve head (ONH) microcirculation, using laser speckle flowgraphy (LSFG) were evaluated. We studied 908 healthy subjects (men = 701, age: 50.0 ± 9.1 yrs, women = 208, 49.8 ± 9.5 yrs, p = 0.76). The average, maximum (Max), and minimum (Min) mean blur rate (MBR) in a heartbeat were evaluated. The parameters were analyzed separately for the tissue, vessels, and throughout the ONH (All). We investigated which MBR sections are correlated with gender and age by univariate and multivariate regression analyses. The Max MBR-All (r = -0.31) was most strongly correlated with gender (men = 1, women = 0). The Min MBR-All (r = -0.24) was most strongly correlated with age, followed by Min MBR-All (r = -0.20). The factors contributing independently to the Max MBR-All were gender (ß = -0.15), pulse pressure, spherical refraction, ocular perfusion pressure, and red blood cell (RBC) count. The factors contributing independently to the Min MBR-Vessel were gender (ß = -0.09), age (ß = -0.25), body mass index, heart rate, and spherical refraction. The factors contributing independently to the Min-MBR-All were age (ß = -0.22), heart rate, and RBC count. Our results revealed that gender differences influence the Max MBR, and aging influences the Min MBR. These correlations were stronger than that of average MBR.

Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway.

Lenvatinib is a multiple receptor tyrosine kinase inhibitor targeting mainly vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF) receptors. We investigated the immunomodulatory activities of lenvatinib in the tumor microenvironment and its mechanisms of enhanced antitumor activity when combined with a programmed cell death-1 (PD-1) blockade. Antitumor activity was examined in immunodeficient and immunocompetent mouse tumor models. Single-cell analysis, flow cytometric analysis, and immunohistochemistry were used to analyze immune cell populations and their activation. Gene co-expression network analysis and pathway analysis using RNA sequencing data were used to identify lenvatinib-driven combined activity with anti-PD-1 antibody (anti-PD-1). Lenvatinib showed potent antitumor activity in the immunocompetent tumor microenvironment compared with the immunodeficient tumor microenvironment. Antitumor activity of lenvatinib plus anti-PD-1 was greater than that of either single treatment. Flow cytometric analysis revealed that lenvatinib reduced tumor-associated macrophages (TAMs) and increased the percentage of activated CD8+ T cells secreting interferon (IFN)-γ+ and granzyme B (GzmB). Combination treatment further increased the percentage of T cells, especially CD8+ T cells, among CD45+ cells and increased IFN-γ+ and GzmB+ CD8+ T cells. Transcriptome analyses of tumors resected from treated mice showed that genes specifically regulated by the combination were significantly enriched for type-I IFN signaling. Pretreatment with lenvatinib followed by anti-PD-1 treatment induced significant antitumor activity compared with anti-PD-1 treatment alone. Our findings show that lenvatinib modulates cancer immunity in the tumor microenvironment by reducing TAMs and, when combined with PD-1 blockade, shows enhanced antitumor activity via the IFN signaling pathway. These findings provide a scientific rationale for combination therapy of lenvatinib with PD-1 blockade to improve cancer immunotherapy.

Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions.

Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or that cause its destabilization to initiate development, are complex and incompletely understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) to simulate single-cell fate transitions and strongly connected components (SCCs) strategy to represent population heterogeneity. This framework was applied to a reverse-engineered and curated core GRN for mouse embryonic stem cells (mESCs) and used to simulate cellular responses to combinations of five signaling pathways. Our simulations predicted experimentally verified cell population compositions and input signal combinations controlling specific cell fate transitions. Extending the model to PSC differentiation, we predicted a combination of signaling activators and inhibitors that efficiently and robustly generated a Cdx2+Oct4- cells from naïve mESCs. Overall, this platform provides new strategies to simulate cell fate transitions and the heterogeneity that typically occurs during development and differentiation.

First report of perfluoroalkyl substances in South African Odonata.

Perfluorinated substances are global and ubiquitous pollutants. However, very little is known about these substances in invertebrates, and even less in terrestrial invertebrates in particular. We analysed adult male dragonflies from six sites in South Africa for perfluoroalkyl substances (PFASs), including perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluro-n-undecanoic acid (PFUnA), perfluoro-n-dodecanoic acid (PFDoA), perfluorohexanoic acid (PFHxA), and perfluorohexane sulfonic acid (PFHxS). PFOS was detected in all individuals, with less quantifiable occurrences of the other substances. The dragonflies from the three northern sites located in farming areas had significantly lower ΣPFASs concentrations than the southern sites located closer to industrial areas (median ΣPFASs of 0.32 ng/g wm (wet mass) for North, and 9.3 ng/g wm for South). All substances except PFOS occurred at similar concentrations at all six sites when quantifiable, but PFOS dominated in the Southern sites. The highest median concentration was from Bloemhof Dam (ΣPFASs = 21 ng/g wm), which is known to be polluted by PFOS. Perfluorinated substances are not known to be manufactured in South Africa, therefore the residues detected are likely to have been derived from imported products. Odonata play a significant role in freshwater ecology. Any impacts on these aquatic and aerial predators are likely to have effects on aquatic and associated ecosystems. Further studies are required over a much larger geographic region and to investigate sources.

CD24 tracks divergent pluripotent states in mouse and human cells.

Reprogramming is a dynamic process that can result in multiple pluripotent cell types emerging from divergent paths. Cell surface protein expression is a particularly desirable tool to categorize reprogramming and pluripotency as it enables robust quantification and enrichment of live cells. Here we use cell surface proteomics to interrogate mouse cell reprogramming dynamics and discover CD24 as a marker that tracks the emergence of reprogramming-responsive cells, while enabling the analysis and enrichment of transgene-dependent (F-class) and -independent (traditional) induced pluripotent stem cells (iPSCs) at later stages. Furthermore, CD24 can be used to delineate epiblast stem cells (EpiSCs) from embryonic stem cells (ESCs) in mouse pluripotent culture. Importantly, regulated CD24 expression is conserved in human pluripotent stem cells (PSCs), tracking the conversion of human ESCs to more naive-like PSC states. Thus, CD24 is a conserved marker for tracking divergent states in both reprogramming and standard pluripotent culture.

Three decades of environmental specimen banking at the National Institute for Environmental Studies, Japan.

After two decades operation of the initial environmental specimen banking, a new program, Environmental Time Capsule Program, started in 2002 as a government-supported long-term program to construct a firm scientific basis for various environmental research studies. The program consists of long-term environmental specimen banking activity and specimen collection of endangered wildlife and is based on cryogenic sample preservation facility called Environmental Time Capsule building, which completed construction in 2004. After 9 years of extensive research, research focuses have been selected and the program was reorganized to the environmental sample collection part and endangered wildlife collection part in 2011. Due to huge environmental disaster caused by the Great East Japan earthquake and the tsunami as well as subsequent nuclear power plant accident at Fukushima, a new sampling and monitoring program started at affected areas in collaboration with the reorganized environmental sample collection and archiving program. Outlines of the quality assurance and quality control (QA/QC) activities in the program and future perspective under related international activities, particularly Stockholm Convention, are reported.

A case of post-mogamulizumab relapse of acute-type adult T-cell leukemia/lymphoma successfully treated with mogamulizumab and etoposide.

A 70-year-old man presented to us with the chief complaints of a generalized rash and a mass in the right clavicular region that he first noticed in the year 2012. Biopsy of the mass led to the diagnosis of cutaneous nodular mass-type adult T-cell leukemia/lymphoma (ATLL) in March 2013. Phototherapy was started, and the symptoms improved temporarily. However, in late June 2013, the serum lactate dehydrogenase (LDH) level increased to 358 IU/L, which was 1.6 times higher than the upper limit of the reference range; based on the findings, transformation of the disease to the acute type was diagnosed. The patient was treated with 6 courses of CHOP therapy (cyclophosphamide, doxorubicin, vincristine, and prednisolone), which resulted in complete remission (CR). However, the rash recurred in late October 2013, and treatment with mogamulizumab was initiated. A total of 8 courses of mogamulizumab were administered, which resulted in CR. The rash and cutaneous nodular masses recurred again in January 2014, and a total of 8 courses of mogamulizumab were administered again starting in February 2014. However, the patient's symptoms began to worsen gradually. Phototherapy was also initiated, but had to be discontinued due to the development of photosensitivity. Treatment with the combination of mogamulizumab and etoposide (25 mg/day for 21 days) was started in May 2014. The nodular mass rapidly decreased in size. The rash or cutaneous nodular mass had not recurred as of August 2014. Thus, combined therapy with mogamulizumab plus etoposide is considered to be effective for resolution of the cutaneous nodular masses in patients with ATLL.

Long-pulsed 1064-nm neodymium:yttrium-aluminum-garnet laser treatment for refractory warts on hands and feet.

Common warts (verruca vulgaris) are the most commonly seen benign cutaneous tumors. However, warts in the hands and feet regions often respond poorly to treatment, some are resistant to more than 6 months of treatment with currently available modalities, including cryotherapy, being defined as refractory warts. We investigated the usefulness of long-pulsed neodymium:yttrium-aluminum-garnet (LP-Nd:YAG) treatment for refractory warts. The clinical trial was conducted on 20 subjects (11 male, nine female) with a total of 34 lesions (periungual/subungual areas, plantar areas, fingers and/or toes). All the subjects suffered from refractory warts despite conventional treatments for more than 6 months. The patients were administrated up to six sessions of treatment, at intervals of 4 weeks between sessions, with an LP-Nd:YAG at a spot size of 5 mm, pulse duration of 15 msec and fluence of 150-185 J/cm(2) . Evaluation of the treatment results at 24 weeks after the initial treatment showed complete clearance of the refractory warts in 56% of the patients. Histological evaluation showed separation of the dermis and epidermis at the basement membrane with coagulated necrosis of the wart tissue in the lower epidermis, as well as coagulation and destruction of the blood vessels in the papillary dermis following the laser irradiation. No scarring, post-hyperpigmentary changes or serious adverse events were documented. Our preliminary results show that LP-Nd:YAG treatments are safe and effective for refractory warts of hands and feet, causing minimal discomfort, and is a viable treatment alternative.

[An endoscopic transnasal transsphenoidal biopsy for pituitary gland Langerhans cell histiocytosis in a child: a case report].

Endoscopic transnasal transsphenoidal surgery is gaining wide acceptance as the first-line treatment of pituitary tumors in adults, as this procedure is minimally invasive and associated with good outcomes. On the other hand, conventional transcranial and sublabial approaches are chosen for infants as their small anatomical structures pose some difficulty. This study reports on the case of a 5-year-old boy who had a Langerhans cell histiocytosis appearing in the sella. The biopsy was performed using the endoscopic transnasal transsphenoidal approach, and the patient has not exhibited any post-operative complications. Although the patient was a fairly young child, the endoscopic transnasal transsphenoidal approach resulted in fewer complications as compared to the transcranial and translabial approaches. Otolaryngologists, therefore, should view this approach more positively. The indication for pediatric skull base diseases can be expected to expand to include endoscopic transnasal surgery.

Dynamic simulation and metabolome analysis of long-term erythrocyte storage in adenine-guanosine solution.

Although intraerythrocytic ATP and 2,3-bisphophoglycerate (2,3-BPG) are known as direct indicators of the viability of preserved red blood cells and the efficiency of post-transfusion oxygen delivery, no current blood storage method in practical use has succeeded in maintaining both these metabolites at high levels for long periods. In this study, we constructed a mathematical kinetic model of comprehensive metabolism in red blood cells stored in a recently developed blood storage solution containing adenine and guanosine, which can maintain both ATP and 2,3-BPG. The predicted dynamics of metabolic intermediates in glycolysis, the pentose phosphate pathway, and purine salvage pathway were consistent with time-series metabolome data measured with capillary electrophoresis time-of-flight mass spectrometry over 5 weeks of storage. From the analysis of the simulation model, the metabolic roles and fates of the 2 major additives were illustrated: (1) adenine could enlarge the adenylate pool, which maintains constant ATP levels throughout the storage period and leads to production of metabolic waste, including hypoxanthine; (2) adenine also induces the consumption of ribose phosphates, which results in 2,3-BPG reduction, while (3) guanosine is converted to ribose phosphates, which can boost the activity of upper glycolysis and result in the efficient production of ATP and 2,3-BPG. This is the first attempt to clarify the underlying metabolic mechanism for maintaining levels of both ATP and 2,3-BPG in stored red blood cells with in silico analysis, as well as to analyze the trade-off and the interlock phenomena between the benefits and possible side effects of the storage-solution additives.

[A case of a large neonatal pharyngeal teratoma].

The congenital teratoma is a rare malformation. We present herein on the case of a large teratoma that arose from the epipharynx in a neonate. The obstructive mass caused maternal polyhydramnios and was identified prenatally by ultrasonography at another hospital. The mother was transferred to our hospital for delivery. We explained about the ex utero intrapartum treatment (EXIT) because of the risk of airway obstruction at birth, but EXIT was refused by the parents. Delivery was accomplished by cesarean section at the 35 th week. Since the newborn had a severe respiratory disorder due to a large intraoral tumor and intratracheal intubation was very difficult, a tracheostomy was done under local anesthesia for 7 min. The tumor was removed successfully on the 9th day and 44th day of age.

Biophysical evaluation of fractional laser skin resurfacing with an Er:YSGG laser device in Japanese skin.

BACKGROUND: Ablative fractional laser skin resurfacing (FLSR) has recently been used for the amelioration of acne scars, and previous studies have shown clinical effectiveness. Despite its extensive use, few studies have focused on the associated changes in biophysical properties of the epidermis. Herein, we evaluate transepidermal water loss, sebum levels, skin hydration, and skin elasticity, following FLSR treatments with an Er:YSGG laser device (Pearl FractionalTM, Cutera Inc., Brisbane, CA), employing non-invasive measurements. METHODS: Five Japanese patients with facial acne scars underwent one FLSR session. Some acne scars appeared to become less obvious as a consequence of the treatment. All patients were aware of a feeling of skin tightness in treated areas. RESULTS: Objective measurements on the lower lateral angle of the eye and on the inner cheeks were evaluated at baseline and at 3 days, 1 week, and 4 weeks after FLSR. Transepidermal water loss showed a significant two-fold (100%) increase at day 3, but had returned to almost the baseline level at week 4 in both areas. Sebum secretion showed a 50% increase at day 3, but had returned to the baseline level after day 7. Skin hydration showed a significant decrease at day 3, but had returned to the baseline level by day 7, and showed significant improvement at the end of the study. Skin elasticity (R2) was still at baseline on day 3, but showed some improvement--an increase of at least 30%--at the end of the study. CONCLUSIONS: Based on our findings, we believe that FLSR should be performed no more than once a month to allow sufficient time for the damaged skin to recover its barrier function in most areas of the face.

Treating onychomycoses of the toenail: clinical efficacy of the sub-millisecond 1,064 nm Nd: YAG laser using a 5 mm spot diameter.

BACKGROUND: Onychomycosis is a relatively common fungal infection. Current treatments have limited applicability and low cure rates. Recently introduced laser therapy has shown to be a safe and effective treatment for onychomycosis. In this study, we evaluate a submillisecond Nd:YAG 1,064 nm laser for treating onychomycoses of the tonail. METHODS: Thirteen subjects (9 female, 4 male) with 37 affected toenails received 1 to 3 treatments 4 and/or 8 weeks apart with a sub-millisecond 1,064 nm Nd:YAG laser. Diagnosis of onychomycosis was confirmed with microscopy. Average follow-up time was 16 weeks post-final treatment. Photos were taken and degree of turbidity was determined using a turbidity scale (ranging from "0 = clear nail" to "10 = completely turbid nail") at each visit. Improvement in turbidity was determined by comparison of turbidity scores at baseline and 16-week follow-up on average. Efficacy was assessed by an overall improvement scale (0 to 4), which combined improvement in turbidity scores and microscopic examination. Overall improvement was classified as "4 = complete clearance" if the turbidity score indicated "0 = clear nail" accompanied by a negative microscopic result. No microscopic examination was performed unless the turbidity score showed "0 = clear nail." RESULTS: Treatments were well tolerated by all subjects and there were no adverse events. Of the 37 toenails treated, 30 (81%) had "moderate" to "complete" clearance average of 16 weeks post-final treatment. Nineteen toenails (51%) were completely clear and all tested negative for fungal infection on direct microscopic analysis. Seven (19%) toenails had significant clearance and four (11%) had moderate clearance. CONCLUSIONS: The preliminary results of this study show this treatment modality is safe and effective for the treatment of onychomycosis in the short term. Additional studies are needed to more fully assess the clinical and mycological benefits as well as optimize the treatment protocol and parameters.

Anesthetic management during tracheotomy in a child with respiratory distress caused by severe intubation-induced glottic stenosis.

We provided anesthetic management during a tracheotomy procedure for a child who demonstrated labored respiration during inspiration because of severe glottic stenosis and bilateral vocal cord paralysis caused by tracheal intubation. A 4-year-old boy developed acute respiratory depression associated with influenza pneumonia and had been under respiratory management with mechanical ventilation with tracheal intubation for 3 days. Following extubation, an upper-airway obstruction immediately appeared. The symptoms later worsened because of development of a common cold, and the patient underwent an emergency tracheotomy. For anesthetic management, we used a combination of ketamine with low-concentration sevoflurane inhalation. The tracheotomy was performed safely without respiratory complications by employing manual-assisted ventilation, while spontaneous breathing was preserved by use of a face mask.