Fine-tuning large language models for chemical text mining.

Extracting knowledge from complex and diverse chemical texts is a pivotal task for both experimental and computational chemists. The task is still considered to be extremely challenging due to the complexity of the chemical language and scientific literature. This study explored the power of fine-tuned large language models (LLMs) on five intricate chemical text mining tasks: compound entity recognition, reaction role labelling, metal-organic framework (MOF) synthesis information extraction, nuclear magnetic resonance spectroscopy (NMR) data extraction, and the conversion of reaction paragraphs to action sequences. The fine-tuned LLMs demonstrated impressive performance, significantly reducing the need for repetitive and extensive prompt engineering experiments. For comparison, we guided ChatGPT (GPT-3.5-turbo) and GPT-4 with prompt engineering and fine-tuned GPT-3.5-turbo as well as other open-source LLMs such as Mistral, Llama3, Llama2, T5, and BART. The results showed that the fine-tuned ChatGPT models excelled in all tasks. They achieved exact accuracy levels ranging from 69% to 95% on these tasks with minimal annotated data. They even outperformed those task-adaptive pre-training and fine-tuning models that were based on a significantly larger amount of in-domain data. Notably, fine-tuned Mistral and Llama3 show competitive abilities. Given their versatility, robustness, and low-code capability, leveraging fine-tuned LLMs as flexible and effective toolkits for automated data acquisition could revolutionize chemical knowledge extraction.

Targeting JMJD1C to selectively disrupt tumor Treg cell fitness enhances antitumor immunity.

Regulatory T (Treg) cells are critical for immune tolerance but also form a barrier to antitumor immunity. As therapeutic strategies involving Treg cell depletion are limited by concurrent autoimmune disorders, identification of intratumoral Treg cell-specific regulatory mechanisms is needed for selective targeting. Epigenetic modulators can be targeted with small compounds, but intratumoral Treg cell-specific epigenetic regulators have been unexplored. Here, we show that JMJD1C, a histone demethylase upregulated by cytokines in the tumor microenvironment, is essential for tumor Treg cell fitness but dispensable for systemic immune homeostasis. JMJD1C deletion enhanced AKT signals in a manner dependent on histone H3 lysine 9 dimethylation (H3K9me2) demethylase and STAT3 signals independently of H3K9me2 demethylase, leading to robust interferon-γ production and tumor Treg cell fragility. We have also developed an oral JMJD1C inhibitor that suppresses tumor growth by targeting intratumoral Treg cells. Overall, this study identifies JMJD1C as an epigenetic hub that can integrate signals to establish tumor Treg cell fitness, and we present a specific JMJD1C inhibitor that can target tumor Treg cells without affecting systemic immune homeostasis.

Loops Mediate Agonist-Induced Activation of the Stimulator of Interferon Genes Protein.

The stimulator of interferon genes (STING) is an important therapeutic target for cancer diseases. The activated STING recruits downstream tank-binding kinase 1 (TBK1) to trigger several important immune responses. However, the molecular mechanism of how agonist molecules mediate the STING-TBK1 interactions remains elusive. Here, we performed molecular dynamics simulations to capture the conformational changes of STING and TBK1 upon agonist binding. Our simulations revealed that multiple helices (α5-α7) and especially three loops (loop 6, loop 8, and C-terminal tail) of STING participated in the allosteric mediation of the STING-TBK1 interactions. Consistent results were also observed in the simulations of the constitutive activating mutant of STING (R284S). We further identified α5 as a key region in this agonist-induced activation mechanism of STING. Free-energy perturbation calculations of multiple STING agonists demonstrated that an alkynyl group targeting α5 is a determinant for agonist activities. These results not only offer deeper insights into the agonist-induced allosteric mediation of STING-TKB1 interactions but also provide a guidance for future drug development of this important therapeutic target.

Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of VZV-Associated Rhombencephalitis.

BACKGROUND: Rhombencephalitis (RE) is a general term for a group of inflammatory diseases of the rhombencephalon caused by different etiologies. Patients of RE caused by the varicella-zoster virus (VZV) are sporadic in medical practice. The VZV-RE is easily misdiagnosed and causes a poor prognosis for patients. METHODS: In this study, we analyzed the clinical symptoms and imaging features of five patients with VZV-RE diagnosed by the next-generation sequencing (NGS) technique of cerebrospinal fluid. Magnetic resonance imaging (MRI) examination was used to characterize the imaging of the patients. The McNemar test was used to analyze the cerebrospinal fluid testing (CSF) values and MRI test of the 5 patients. RESULTS: We finally used NGS technology to confirm the diagnosis in 5 patients with VZV-RE. MRI revealed T2/FLAIR high signal lesions in the patients' medulla oblongata, pons, and cerebellum. All patients had early signs of cranial nerve palsy; some had herpes or pain in the corresponding cranial nerve distribution areas. The patients develop headaches, fever, nausea, vomiting, and other signs and symptoms of brainstem cerebellar involvement. McNemar's test showed no statistical difference between multi-mode MRI and CSF values for diagnosing VZV-RE (p = 0.513). CONCLUSIONS: This study showed that patients with herpes in the skin and mucous membranes at the distribution area of the cranial nerves and with the underlying disease were prone to RE. We suggest that the NGS analysis should be considered and selected based on the level of parameters, such as MRI lesion characteristics.

Computing the relative binding affinity of ligands based on a pairwise binding comparison network.

Structure-based lead optimization is an open challenge in drug discovery, which is still largely driven by hypotheses and depends on the experience of medicinal chemists. Here we propose a pairwise binding comparison network (PBCNet) based on a physics-informed graph attention mechanism, specifically tailored for ranking the relative binding affinity among congeneric ligands. Benchmarking on two held-out sets (provided by Schrödinger and Merck) containing over 460 ligands and 16 targets, PBCNet demonstrated substantial advantages in terms of both prediction accuracy and computational efficiency. Equipped with a fine-tuning operation, the performance of PBCNet reaches that of Schrödinger's FEP+, which is much more computationally intensive and requires substantial expert intervention. A further simulation-based experiment showed that active learning-optimized PBCNet may accelerate lead optimization campaigns by 473%. Finally, for the convenience of users, a web service for PBCNet is established to facilitate complex relative binding affinity prediction through an easy-to-operate graphical interface.

Acute invasive mucormycosis rhinosinusitis causing multigroup cranial nerve injury and meningitis-A case report.

This study reported a case of a Rhino-Orbital-Cerebral Mycosis (ROCM) patient with multiple groups of cranial nerve damage as the primary clinical manifestation, confirmed by histopathology and cerebrospinal fluid metagenomic next-generation sequencing (mNGS) technology. Relying on the MRI3D-SPACE technology, we observed the location and extent of the cranial nerve damage in the patient. The results suggested that fungal meningoencephalitis caused by mucor may enter the skull retrograde along the cranial nerve perineurium. The patient was admitted to the hospital with a preliminary diagnosis of mucormycosis infection after 1.5 days of mouth deviation. We treated the patient immediately with intravenous amphotericin B liposomes. After 21 days of hospitalization, the clinical symptoms of the patient did not improve significantly. The patient was discharged due to financial difficulties and antifungal treatment at home, and his disease had stabilized at the 6-month follow-up.

Case report: A variant of wall-eyed bilateral internuclear ophthalmoplegia from unilateral pons infarction.

Wall-eyed bilateral internuclear ophthalmoplegia (WEBINO) is an uncommon ocular motility disorder that encompasses the following clinical signs: bilateral adduction deficits, bilateral abducting nystagmus, convergence lost, and a large angle exotropia in primary gaze. Here we report a case of a 55-year-old man presenting with atypical WEBINO syndrome with unilateral exotropia. The coverage test was used to record the patient's alternating exotropia. The patient experienced diplopia and ophthalmoplegia and was admitted to our hospital 3 days after the onset of the double vision. Neurologic examination showed left eye exotropia and bilateral internuclear ophthalmoplegia with impaired convergence. Vertical saccades of the left eye were also limited. Consequently, an MRI scan suggested an acute infarction in the left of the pontine tegmentum. The patient was finally diagnosed with pons infarction and was treated with anticoagulation and anti-platelet aggregation therapy.

Analysis of Cases with Cerebrospinal Fluid Characteristics Similar to Tuberculous Meningitis.

Purpose: The diagnosis of tuberculous meningitis (TBM) is difficult and relies on the patient's clinical presentation and initial cerebrospinal fluid testing. Treatment outcomes for some patients with early consideration of TBM meningitis are often poor. Patients and Methods. In this study, we retrospectively analyzed 24 non-TBM patients whose early changes of cerebrospinal fluid were similar to those of TBM through the second-generation cerebrospinal fluid sequencing technology. Results: All patients included in this study had an acute onset, including 5 patients with a history of upper respiratory tract infection, 9 patients with fever, 6 patients with headache, 5 patients with psychiatric symptoms, 6 patients with cognitive impairment, 9 patients with signs of meningeal irritation, and 6 patients with seizures. Sixteen patients presented with altered content and level of consciousness during their admission. The leukocyte counts (median, 124.0 × 106/L) and total protein concentrations (median, 1300 mg/L) were higher than normal reference values in all patients, whereas glucose (median, 1.345 mmol/L) and chloride concentration values (average, 111.7 ± 5.2 mmol/L) were lower than normal reference values. The patients included 2 cases of Liszt's meningitis, 2 cases of Brucella infection in the CNS, 4 cases of Varicella zoster virus encephalitis, 2 cases of human herpes simplex virus type 1, 2 cases of lupus encephalopathy, 2 cases of anti-NMDAR receptor encephalitis, 2 cases of meningeal carcinomatosis, 5 cases of cryptococcal meningitis, 2 cases of CNS sarcoidosis, and a case of invasive Rhizopus oryzae infection. All patients were tested for NGS in cerebrospinal fluid. Eight patients were diagnosed with anti-NMDAR encephalitis, meningeal carcinomatosis, lupus encephalopathy, and CNS sarcoidosis. Nine patients experienced death; 15 patients had a good prognosis and left no significant sequelae. Conclusion: The analysis of patients with TBM-like cerebrospinal fluid changes will help improve the diagnostic accuracy of the disease and reduce misdiagnosis and underdiagnosis.

Four patients with infarction in key areas of the Papez circuit, with anterograde amnesia as the main manifestation.

The Papez circuit is an important brain structure that is closely associated with learning and memory. In this report, we present four patients with anterograde amnesia as the main manifestation induced by Papez circuit infarction. In addition, we review the distribution of the responsible arteries in key and rare regions to investigate the pathogenesis of these infarctions.

A case of varicella zoster encephalitis with glossopharyngeal and vagus nerve injury as primary manifestation combined with medulla lesion.

Varicella zoster virus (VZV) can invade the brainstem or brain via the glossopharyngeal, vagus , or facial nerve, resulting in brainstem inflammation or encephalitis. We report the case of a 66-year-old male patient with a primary manifestation of medulla injury of the glossopharyngeal and vagus nerves, combined with a medulla lesion, who was misdiagnosed with lateral medullary syndrome. Facial nerve injury and earache subsequently occurred and human herpes virus 3 (VZV) was detected by second-generation sequencing of the cerebrospinal fluid. The final diagnosis was varicella zoster encephalitis, which improved after antiviral therapy.

A case of surgically-associated anti GQ1b antibody syndrome accompanied by saccadic ping pong gaze.

BACKGROUND: Periodic alternating ping-pong gaze (PPG) is a rare disease with few reports. To our knowledge, there was no report on anti GQ1b antibody syndrome accompanied by PPG. This paper reported a case of anti GQ1b antibody syndrome with Bickerstaff's Encephalitis (BBE) overlapping classic Guillain-Barre Syndrome (GBS) after aortic valve replacement, accompanied by an excessive PPG in the course of diagnosis and treatment, this was indeed rarely. CASE PRESENTATION: A 55-year-old male patient was admitted to our hospital with intermittent chest tightness for 3 months, and his condition has worsened in the past 10 days. Aortic valve replacement was performed because of the existence of the moderate and severe stenosis of aortic valve. Horizontal movement of the eyeball was involuntarily slow. The eyeball hovered and returned from one side to the other horizontally for 3-4 s per cycle. In combination with the patient's typical clinical and laboratory tests, the final diagnosis was anti GQ1b antibody syndrome BBE combined with GBS, accompanied by saccadic ping pong gaze. Intravenous immunoglobulin (0.4 g/kg) was given for immunomodulation, methylprednisolone (1000 mg) therapy and symptomatic treatment were performed in the patient. CONCLUSIONS: The patients were discharged from hospital on the thirtieth day because of economic reasons. After 6 months of follow up, the patients left behind a lack of fluency in speech and limb mobility, but the basic life can be taken care of by himself.

Successive occurrence of vertebrobasilar dolichectasia induced trigeminal neuralgia, vestibular paroxysmia and hemifacial spasm: A case report.

RATIONALE: Study reported an extremely rare case of trigeminal neuralgia, vestibular paroxysmia, and hemifacial spasm successively occurring in a patient with vertebrobasilar dolichoectasia (VBD). PATIENT CONCERNS: A 66-year-old female patient presented with episodic vertigo for 20 days before she was admitted to our hospital. Vertigo suddenly occurred when the patient rotated her head 20 days ago, the symptoms of vertigo were improved after continuous 1 to 3 seconds, and similar symptoms were repeated in sleep and rest, with a frequency of 30 to 40 times per day. The patient had a history of hypertension with poor blood pressure control for more than 20 years. DIAGNOSES: The final diagnosis was vertebrobasilar dolichectasia, right trigeminal neuralgia, and vestibular paroxysmia. INTERVENTIONS: Vitamin B1 (10 mg), methylcobalamin (0.5 mg), and carbamazepine (0.1 g) were given orally 3 times a day to relieve the symptoms. OUTCOMES: On the seventh day of drug treatment, the symptoms of paroxysmal vertigo and trigeminal neuralgia were completely relieved, but occasional episodes occurred during the follow-up period. Five months after discharge, right hemifacial spasm appeared in the patient, which did not affect the quality of life of the patient, so the patient did not choose further treatment. Six months after discharge, the patient was lost to follow-up. LESSONS: Comprehensive treatment to control VBD risk factors, delay the progression of VBD, and improve clinical symptoms may have a better effect on such patients. However, further research is needed.

Spinal dural arteriovenous fistula presenting with subarachnoid hemorrhage: A case report.

RATIONALE: Subarachnoid hemorrhage (SAH) is a common and serious disease and one of the most important differential diagnoses in the emergency department. PATIENT CONCERNS: A 39-year-old female patient with a 12 years' history of migraine, presented with a sudden headache combined with motor aphasia. Physical examination suggested probable positive neck resistance. SAH was confirmed by magnetic resonance imaging. In addition, spinal digital subtraction angiography and spinal vascular computed tomography angiography indicated spinal arteriovenous malformation (SAVM). DIAGNOSES: The final diagnosis was spinal dural arteriovenous fistula presenting with SAH. INTERVENTIONS: Following diagnosis, appropriate drugs were administered, but the therapeutic effect was poor. Then the patient was then transferred to a superior hospital where she was treated with interventional embolization. OUTCOMES: Through 2 years of follow-up, intermittent migraine was found in the patient, but the symptoms of occipital pain, nausea, and vomiting did not occur again. LESSONS: For patients who have been diagnosed with SAH but have no definite cause, we should pay attention to the etiological screening of SAH, and the possibility of the spinal cord SAH should be vigilant. The pain in the chest and back and the signs of spinal cord may be an important breakthrough in patients with spinal cord SAH, and medical history and physical examination are particularly important.

Lateral medullary infarction with similar features of Brown Sequard syndrome caused by vertebrobasilar dysplasia and Klippel-Feil syndrome: A case report.

RATIONALE: Patients with Klippel-Feil syndrome (KFS) are always anomaly associated with vertebrobasilar dysplasia. That may present commonly as infarction of brainstem, medulla, and cerebellum. In this article, we reported a rare case of lateral medullary infarction (LMI) with similar features of Brown Sequard syndrome caused by vertebrobasilar dysplasia and KFS, and the 2 rare conditions that are causally related. The case is being reported because of its unusual and rare presentation. PATIENT CONCERNS: A 38-year-old female presented with acute unsteadiness, along with a tendency to lean to the left side while walking or sitting, and paresthesia in the right lower limb and trunk, at 2 days before admission. She had no history of hypertension and diabetes, but had a 20 years history of neck pain and dizziness, which was related to head movement. DIAGNOSES: Brown Sequard syndrome and a lesion of the left thoracic spinal cord were suspected initially. KFS was confirmed by the cervical magnetic resonance imaging (MRI) and computed tomographic angiography (CTA) results. Transcranial Doppler (TCD) results confirmed that there was a causal link between LMI and KFS. INTERVENTIONS: The patient rejected the operation of stabilization of the cervical spine with fusion at appropriate levels. OUTCOMES: No recurrence of stroke, but neck pain and dizziness remained after 6 months of discharge. LESSONS: For such patients, the conventional treatment of cerebral infarction might be ineffective, but stabilization of the cervical spine with fusion at appropriate levels can successfully prevent further episodes of syncope and stroke.

Miller Fisher syndrome with acute angle-closure glaucoma as the first manifestation: A case report.

RATIONALE: There were no reports of Miller Fisher syndrome (MFS) with acute angle-closure glaucoma as the first manifestation. PATIENT CONCERNS: A 78-year-old female patient was admitted to our hospital with pain in her left eye, blurred vision along with nausea, and vomiting for 2 days. It was extremely rare that ophthalmoplegia, loss of tendon reflexes, and ataxia, did not occur in the early stages of MFS, and initial presentation was only dilated pupis and an increase in intraocular pressure. DIAGNOSES: The final diagnosis of the patient was MFS. INTERVENTIONS: Intravenous immunoglobulins were administered. OUTCOMES: Ophthalmoplegia, walking instability, and ataxia gradually improved. At 3 months follow-up, there was no neurological deficit, and the patient could completely self-care. LESSONS: This is the first report of MFS patient with acute angle closure glaucoma as the first manifestation. Consideration should be given to the possibility of incorporating autonomic nervous system dysfunction, or even MFS, in patients with acute angle-closure glaucoma in order to reduce missed diagnosis rate.